"I may have at least a partial answer for you.
Important question is....when you boot and look in system profiler at "About This Mac" is the 7950 ID'd as "AMD Radeon 7xxx" or "AMD Radeon 7950"?
I just recreated your problem, quite repeatable, but only when the rom switch is in PC position, ie booting via self initing drivers.
If in the EFI position, it works fine. I have a 24" Apple LED and a 27" Apple LED running 10.9.2.
It is bad enough in PC position that just connecting the Apple Display causes machine to crash and reboot.
Here's a picture from the Sapphire instructions on the Radeon 7950 Mac Edition switch:
A reply to his post from another 7950 owner said that fixed his problem. (Card was set to PC position.) Not sure how common that is but from previous threads, more than a few likely are. (It may have been set to PC from the factory and never changed when installed by some owners.)
[The switch position of course has no effect on performance. (Which reportedly is lower w/10.9.2 drivers.) Hopefully improved in the next update.]
(FYI: A later post in the above thread from another Sapphire Radeon 7950 owner reported his switch seemed to be wired in reverse - he said with it in the correct position per the manual, the OS X System info reported it as "Radeon 7xxx", reversing the switch resulted in "Radeon 7950" ID. And later another user said their card also appears to be reversed from the earlier info. (Changes in some production runs?) Of course if your card is working ok, don't change anything. If you find DisplayPort output is not working in OS X 10.9.2, try changing the switch position.)
BTW: For cards that do not have a bios switch, the 10.9.2 drivers seem to only work via DVI port as mentioned in earlier threads below. Reported to Apple but no idea if they'll fix it (even in 10.9.3). A thread below on the subject has info on driver mods (revert/replace) and some have reverted back to a 10.9.1 via Time Machine or a backup/other OS installed on another Mac Pro hard drive.
Threads on OS X 10.9.2 Problems/Tips:
(includes links to Apple forum threads on 10.9.2 problems, granted some are not common but posts may have tips for those that have similar issues. And anyone with a similar setup can post if they've had a problem or not and any suggestions that may help.)
For those that had problems, it would be good to know how they updated (SU/Delta, Delta or Combo updater) and if any 3rd party addons are installed. (Personally I wish that all security updates were separate releases instead of bundled in other updates for those that only wanted the security fixes.)
Late 2013 Mac Pro SMC Firmware Update 2.0 (info/download/tips)
iTunes 11.1.5 update (bugfixes)
Xcode Update for OS X Server (Mavericks 10.9.2)
Freeware VM VirtualBox 4.3.8
2013 Mac Pro 6-core ($3999) Review
CalDigit T3 (Thunderbolt enclosure) Review
OWC Adds Independent Mode to Elite Pro Qx2v
Steam Client Update (has one OS X fix listed)
Updated Apple Support/How-To/Troubleshooting Articles:
- EFI and SMC firmware updates for Intel-based Macs
- Mac Pro (Late 2013): Using multiple displays
- Using multiple displays in Mavericks
- OS X Server: How to prevent sleep
- About Safari Internet plug-in management
- Using captioning features in Mavericks
- About the new iWork for Mac Features and compatibility
- Keeping Junk folder consistent between iCloud Mail & OS X Mail
- About Disney Movies Anywhere and iTunes Store