It is actually the handoff between OS and BIOS. This is why in Mavericks I had all 32GB show up perfectly and was able to put in my two other video cards without a problem. If I were to do the same things in Windows, I'd have no problem because windows has every interpretation know to man for hardware configuration in the slots handed off by the BIOS. Matter of fact, your SMBIOS, in addition to the rest of the DSDT, is in charge of telling the OS what your motherboard has and how it works. The trouble is, it doesn't always translate well because OS X is obviously specifically programmed for the boards that only Apple makes.
Perhaps trying the video card on a slot controlled by the second processor or using slots 3, 5, 7.
After looking at the block diagram in the back of the manual I saw that PCIe x16 slots 1 and 3 are controlled by CPU 1 and slots 5 and 7 are controlled by CPU 2. So, I thought maybe having the cards on separate CPUs might be the problem. I'm partially right.
I put the cards in slots 5 and 7 and could boot up with both cards. However, it only recognizes one card correctly, while the other card just says NVIDIA chip model. Also weirdly enough, I could only plug the monitor into the bottom card; otherwise plugging it into the top card would prevent the bootloading from ever passing the PCI configuration begin.
I will be trying slots 1 and 3 today but I'm not expecting much success. I'm thinking that a DSDT edit is needed to get this working the right way.
I feel you about the difficulty in knowledge and how to get it, it appears that it's all out there in 1000 different threads and you just have to find it.
That pretty much sums it up.
By the way, if you haven't already found this thread
http://www.tonymacx86.com/user-buil...xeon-e5-2660-gtx-590-3gb-64gb.html#post583729
it also provides a wealth of information.