I'm not sure what the root problem is, but since I've not seen this nor remember any other mails that I recall in the past about it, I wanted to ask for reader feedback. (He thinks I have a "magic" Mac Pro since I've never seen that problem.)
I asked for feedback from 2009 Mac Pro with any PCIe eSATA card and have bootcamp/windows drives installed, and if they've seen any problems booting to the BC/windows drives.
In case it matters, I asked to include the following:

• Your Mac Pro's Bootrom and SMC versions (from apple system profiler),
• If it's a Quad or 8-Core 09 Mac Pro
• Details on Drives used (ASP will list drive firmware version as 'revision') and Bays used
• Any Apple Bootcamp updates applied or not, Windows versions, etc.
• Info on eSATA Card models used and slot used
• Any other PCIe cards installed
• Info on any connected devices (wired or BT/Wireless)

I've booted to my BC drives hundreds of times w/o any problems personally, but since that reader mentioned problems with multiple cards I'm curious what could be the cause. I've used the upper/top PCIe slot for the card. Both of them have had no problems in my experience in any OS I have installed (10.6.x, 10.5.x, Vista and Win7) so far. I've used the NT 6G (non-PM) card for about 6 months to date. My Bootcamp HDs are a Seagate (7200rpm) 1.5TB (BC partition is 1TB) and an original 7K1000 1TB Hitachi (BC drives in Bay 3 and 4). And if it matters, my NT 6G (non-PM) card reports bios 1.0.0.1003 IIRC. (Will double check that.) The first reader with the problem said it was seen with 4 different cards - I wrote him to ask for the above details also.
BTW - Had one reply from a Quad-Core owner so far that said he's seen this problem about 25% of the time. (Almost made me wonder if it's a drive ready issue since it wasn't 100% of the time.)

My Info (I've seen no problems with my setup with either of the 2 cards I've used):

• Early 2009 Mac Pro 8-core (dual 2.66GHz CPUs - shipped spring 2009)
• 12GB RAM (6 x 2GB - OWC upgrade kit bought in spring 2009)
• Bootrom: MP41.0081.B07, SMC: 1.39f5
• Until appx May 2010, I had dual Optical drives, the OEM LG GH41N 'superdrive' that shipped in it + an LG Blu-Ray burner/HD-DVD reader/DVD burner. (The latter was moved into an OWC quad-interface external case so it could be used w/other machines.)
• Drives Used:
  • Bay 1 (OS X 10.6.4): 1.5TB Seagate ST31500341AS, firmware CC1H. (OS X 10.6.4 on partition 1 (1.07TB), Partition 2 is OS X formatted "spare", partition 3 is a FAT32 volume for easy file copy/sharing from any boot OS.)
  • Bay 2: (OS X 10.5.8) WD Caviar Black 1TB
  • Bay 3: (Vista 64bit Ult.) Seagate 1.5TB (same model/firmware as above - single partition)
  • Bay 4: (Win 7 Pro 64bit) Hitach 7K1000 1TB (first 1TB model), firmware GKAOA70M
• Windows 7 has last Bootcamp update from apple, Vista doesn't
• eSATA cards I have used: (booted to Windows/used them both OK - top PCIe slot used)
  • NewerTech 6G (non-PM) card, bios v1.0.0.1003 (used since late Jan 2010)
  • Dynex (Sil3132 based) 2 port eSATA card (used until late Jan 2010)
• Other PCIe Cards installed: Only Nvidia GTX-285 (graphics card)
• Info on any connected devices: USB Logitech G15 keyboard, Logitech Revolution MX mouse (RF/wireless) and of course a display (DVI Samsung 2493hm)

Some History:
Originally I had only a Vista (64bit Ult) Bootcamp HD (installed appx May 2009 IIRC), then in late August 2009 I bought a $20 Sil3132 eSata card for tests with Snow Leopard (ref: cheap eSATA cards w/OS X 10.6 article) - it booted to windows fine, worked in windows, etc. When Windows 7 was released (retail) in October 2010, I installed a Windows 7 Upgrade to a separate hard drive, using the (discounted) 3-license Windows 7 home premium upgrade pack. I installed Win 7 to a different drive for 2 reasons:

1. I wanted a 'clean' install of Win 7 (not upgraded over Vista)
   and
2. Windows Home Premium does not support dual CPUs and I didn't want to lose dual CPU support I had in Vista. About a month later I picked up a Win 7 Pro "Upgrade" and applied that over the Win 7 HP install.

To boot to Windows 7, I select the Vista HD which gives me the option to select either Vista or Win 7. (This menu was present after the win 7 'upgrade' to a separate drive, it is not something I installed or a 3rd party addon.)
After reviewing the NewerTech 6G card in late January 2010, I bought it. (No OS X drivers needed, faster than the 3132 card, native support in 64bit Snow Leopard, etc as noted in the review. Since that review 64bit Sil3132 drivers were released, but I'm not going back to that card.)
I have booted to Windows/bootcamp HDs probably a hundred times and have had no issues with either card.

Dave's System Info (problems booting to BC/Windows with 4 different eSATA cards installed): Here's the system/config details from the reader that said he's unable to boot to bootcamp/windows volumes with any of the 4 eSATA cards he's tried in his 2009 Mac Pro.

• Early 2009 Mac Pro 8-core (dual 2.66GHz CPUs)
• 16GB RAM (6 x 2GB - OWC upgrade kit bought in spring 2009)
• Bootrom: MP41.0081.B08 (Emphasis mine, My earlier shipped Mac Pro has bootrom .B07), SMC: 1.39f5
• Details on Drives used (ASP will list drive firmware version as 'revision') and Bays used. (This may or may not be a factor but while we're doing this I wanted as much detail as possible.)

  "I get the problem regardless if any drives are connected to the eSata card. I even get the problem if I try to boot a Windows or Linux boot CD with no drives attached to the computer at all. Internally, I am using a hard drive (connected directly to the motherboard) that has OSX/Windows (bootcamp partition on the OS X drive), an Hitachi 1TB, revision ST0BA36A (came with the mac), ~900GB for OSX and ~100GB for Windows 7 64-bit. I've also used a 1TB Western Digital WD1002FBYS with only Windows 7 64-bit installed."

• Boot Camp Assistant v. 3.0.2 (314) on the OSX side, Boot Camp 3.0 and 3.1 in Windows.
• eSATA cards tried: All cards used in slot 4 (top slot). The Newertech card was also installed in slot 3.
  • NewerTech eSATA 6G PCIe 2.0 RAID/PM card
  • Rosewill RC-218 (Marvell 88SX7042 chipset)
  • Wiebetech 30310-0500-0002 (PCIE-2S) (3rd one down) - SI3132 chipset
  • Can't remember or find the 4th card. On a side note, I tried a firewire card which worked fine in both Windows and OSX.
• Other PCIe Cards installed: Just an ATI 4870 (graphics card)
• Info on any connected devices: Keyboard, mouse, monitor, no bluetooth.

(from his July 15th email)
"What I can do:
I can boot to a hard drive with OSX installed, just not the Windows side. I can also boot to a OSX install CD or Netboot an OSX image.

With the card installed (no drives connected), I cannot boot to any Windows/Linux installation or CD.

I've got two threads open, and I might post a link to your site in both of them so maybe other folks can chime in.

http://discussions.apple.com/thread.jspa?threadID=2502591

http://forums.macrumors.com/showthread.php?t=964128
No replies on this thread yet.
I also have a support ticket open with Apple. The guy I talked to had a chat with the engineers and they gave 2 options to try:

1. reinstall Windows but load the drivers during the install. This didn't work when I tried it

2. remove the "drive launch" option from the boot.ini file because the card is trying to make some kind of irq request. Windows 7 doesn't have a boot.ini file, but it's equivalent "bootmgr" file does not have a "drive launch" option. So, this attempt didn't work either.

I will call the guy back at Apple in 2 weeks after he gets back from vacation. Thanks again for your help, Mike.
-Dave"

Update: Dave later wrote that tests with another Mac Pro w/B07 bootrom (like mine, vs his B08 mac pro) booted to BC/Windows volumes OK with the same eSATA card(s). So the question is if there is anyone with a ".B08" bootrom Mac Pro that doesn't see this problem?

There was one other reply to the post/request in the July 15th news page from a 2009 Mac Pro owner with a NT 6G RAID/PM card that said he has the problem (booting to his BC/Windows 7 drive) appx 25% of the time. I asked him for the details on his system/config (the items listed above) and got this reply late friday night (23rd)

"Ok I'm back from Venice, LA for a while...
This is actually what is happening.... When the drives are attached and rebooting the system..... the fans increase (normal) (no fan control is active, fans default to failsafe mode) but for about 15 seconds.... then it takes about 45 seconds for the boot splash screen to appear for OSX or Windows 7 to start up.. based on what I selected in systems preferences.
When I gave you the 25 percent number I was not giving it time to reboot... I thought the system was hung.... then I would unplug the drive.... etc...

If I leave the card installed but disconnect the Firmtek enclosure with the drives, then everything boots as normal. (since the NT 6G card has a bios/checks for connected drives at startup, that is likely cause for additional delay. At windows DOS boot screen the card/BIOS version is displayed and then a check is run of any connected drives. (it will report if no drive found or the ID/info of a connected drive.))

Here is my system info.

I am using Slot 4 for the NewerTech MAXPower eSATA 6G PCIe 2.0 Controller Card (card bios v1.0.0.1003)
eSATA Drives are installed in FirmTek SeriTek/2EN2 enclosure. eSATA Enclosure Drives info: 1 TB Seagate ST31000340AS (Firmware SD1A). I have also tried a Western Digital 320 WD3200AAKS-00UU3A0 (firmware 01.03B01)
(I was more interested in the internal drives/BC drive in case that was a factor (delay/drive ready, etc.). The reader with this problem (100% of the time he said) said he still had the problem w/o any eSATA connected drive. The suspect now is if his later B08 bootrom version is a factor.)

Mac Pro info....

Model Identifier: MacPro4,1
Processor Name: Quad-Core Intel Xeon (single CPU)
Memory: 6 GB
Boot ROM Version: MP41.0081.B07
SMC Version (system): 1.39f5
SMC Version (processor tray): 1.39f5

Let me know if you want more info...
Mark G."

I have this same card (which has same card bios version) and have seen no problems booting to my BC/Win drives, even if I have a connected eSATA drive - typically a data (not OS boot) drive. However my eSATA drive case typically used is a pure SATA one - OWC dual-drive eSATA only case. (I mentioned/linked to that case in my original review of the NewerTech 6G (non-PM) card back in January.) I've used an HD dock with the card as well, but can't recall now if I booted to windows with it connected/HD inserted in it. (I'll try that.)
However there's been a long history of eSATA case/bridge board issues with some SATA cards as mentioned many times over the years. (Noted in the article on using spare pre-2009 Mac Pro motherboard SATA ports for eSATA, expresscards page, card vendors pages, even SATA controller chip driver pages (like Silicon Image's). This is why I included a data corruption test in the review. (Sometimes issues are so bad the ext drive can't be used, but sometimes it may appear to be ok, but actually have intermittent data corruption.)

Other Reader Replies: (Initially it was thought it may be related to the bootrom version but that may not be so based on some other owner's comments - i.e. some w/B07 have seen the problem and one with B08 bootrom hadn't.)

(from Aug 27th 2010 email)
I just heard back from a contact at Apple and they are working on the problem. They just released a fix for MacBook Pros, which I didn't know they had an issue. (FYI: As reported on the Expresscard reports page here since late 2008, the Unibody MBPs don't seem to work with any eSATA expresscard in Windows. Resource errors reported. One reader tried 5 or 6 different cards (tried two - SIL3132 and JMB360 based ones, neither worked in Windows.) Not sure if any later updates fixed that or if the 2010 MacBook Pros work.-Ed)
He said the Mac Pro problem is being worked on, but he doesn't know when it'll be fixed.
But the good news is that it WILL be fixed!
Thanks again for all your help. Couldn't have done it without you.
-Dave"

I hope there is a fix for this (and the root cause known).
(clip from the Dec 7th, 2010 news page)
Although it was thought that the bootrom version (B08 vs B07) was the reason for some 2009 Mac Pros not being able to boot to bootcamp/windows volumes with an SATA card installed, recently a reader sent notes he's seen the opposite - his B07 bootrom mac pro has the problem, but not his B08 bootrom Mac Pro. He said he reported the problem to Apple and was hoping for a callback.
As I mentioned earlier, I've never seen this problem with a B07 (spring 2009 shipped) Dual 2.66GHz 2009 Mac Pro using either a NewerTech 6G (non-PM/natively supported card version) or a Sil3132 based eSATA card installed. (Booting to separate internal HDs with Win7 Pro/64 and Vista Ult/64 works.)
If the bootrom version isn't the cause/factor, I'm not sure what is.
(If anyone with a 2010 Mac Pro has an SATA card installed and bootcamp volume(s), let me know if you've seen any issues booting to them.)

(added 1/15/2011, from 1/14/2001 email)
"Mac Pro Info (from apple system profiler)

• Model Identifier: MacPro4,1
• Processor Name: Quad-Core Intel Xeon
• Processor Speed: 2.26 GHz
• Number Of Processors: 2
• Total Number Of Cores: 8
• L2 Cache (per core): 256 KB
• L3 Cache (per processor): 8 MB
• Memory: 6 GB
• Processor Interconnect Speed: 5.86 GT/s
• Boot ROM Version: MP41.0081.B07
• SMC Version (system): 1.39f5
• SMC Version (processor tray): 1.39f5

I've tried 2 SIL3132 cards. Once came with my SansDisk PM case the other a $20 Rosewill RC-219 R card from NewEgg. I've also tried RAID CARD HIGHPOINT|ROCKETRAID2314 and Rocket 622. All gave me similar issues. They would work great in OSX but windows screen would remain black when booting to Win 7. (Tried holding option button and selecting drive and refit)

Win 7 Home is installed on an internal sata drive and has its own dedicated drive. (not a partition)

Here's the weird part. The Rosewill card booted to Win 7 when I first installed the card. Right after I connected the PM case it would no longer boot. Drives attached or not! I tried several times just to be sure because I would have no problem disconnecting the eSata cable the few times a week I boot to Win7. But no. It stays black no matter what. (And I waited and waited)

Is there any way to update the bootrom to solve this issue? (Not that I've seen - no updates released by apple to date (as of Jan 2011))
Has Apple acknowledged the issue? (not publicly, although one reader back in Aug 2010 (copy below) said apple support told him they were aware of it and it would be addressed in a future update. No proof of that however.)
I know this is an old article but I just stumbled upon it. Please let me know if you have any more info, or if you need any more info from me.
-Mano"