" Last night I finally got around to upgrading the cpu in my mid-2010 Mac Pro to a W3690 (3.46GHz, 6 cores, 12MB cache, 130W TDP) Intel cpu as per the excellent mac rumors forum roadmap by phillip ma. I am beta testing OS X El Capitan, so I was prepared for failure or discrepancy of some type, but after installation and restart geek bench 3 showed 2665 single core and 15029 multi-core scores... great results, right? For some reason however I paid for the increase in score with the loss of ram slot 1's 16 GB.

(RAM shown as "0 MHz"? Geekbench bug?)

I switched out the 2 ram modules and both worked, but only in slot 2. (Can you verify that slot 1 is OK?) I read a couple of forum notes which said that the W3690 was initially only able to handle 31GB of ram, and a tech at OWC (whose 2 x 16GB sticks of ram I have installed) went to the Intel site in response to a tech enquiry from me and said the product was supposed only to perform properly, at first release, with a paltry 8GB of Ram. Anyway I searched intel's support site and found a windows and linux version of their cpu diagnostic but not anything about a version for the mac, hoping such software might point up the problem.
(FYI: Intel's W3690 specs lists 24GB Max Memory Size, "dependent on memory type". (Maybe based on 3 slots x 8GB dimms when spec was done?) Apple offered a CTO 3.33GHz 6-core as an option for the single CPU Mid-2010 (and Mid-2012) Mac Pros, which I assume is the Intel W3680. The W3680 specs list the same 24GB max memory as the W3690. (W3680 spec lists 36-bit physical address extensions, W3690 spec lists 40-bit.)
OWC's maxram page shows despite Apple listing 32GB max for 2010 6-core (single cpu, 4 dimm slots), they tested 48GB max using OE CPUs. (Often Apple's max specs aren't changed when larger capacity dimms become common, even if they work fine.) The July 2014 news had a report on a W3690 CPU upgrade, but he was using 3x8GB dimms (24GB). 3 identical dimms per CPU enables triple-channel mode. Using 2 or 4 like dimms run dual-channel.)

I was also told by another owc tech earlier that if a pram or cpu (SMC?) reset did not work, it was probably a malfunction of the W3690. I joined the macrumors forum but as of this writing have not received a confirmation email so I can post and try to get hold of phillip ma or someone who can help me understand what has happened here. I am able to use my computer and everything works except memory slot 1.
(Is a single 16GB dimm in slot 1 (other slots empty) not recognized? To confirm slot 1 is working.)

Mid-2010 Mac Pro, 16GB ram, one 480GB ssd, 3 various sized internal sata hdds, running El Capitan beta 3. (It runs very well, only two minor feedback notes.) I got the cpu on eBay for less than $300.
-Gene H."

Hopefully there's no problem with your CPU or dimm slot. If you confirm 32GB isn't supported, then I'd try 3x8GB instead if you could exchange/swap the 16GB dimms. (Triple-channel memory config instead of dual-channel with a pair of dimms.)

(The June 26th news had notes on a 2009 Mac Pro (flashed to Mac Pro 5,1 bootrom) that upgraded to a single X5690 3.46GHz CPU (from ebay) using 32GB ram. Didn't mention if 16GBx2 or 8GBx4.)

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