DIMMs must be placed in exactly the right arrangement in a Mac Pro or you'll lose access to some of the RAM. And, confusingly, the arrangement is different among different years/models!Here's a memory issue that I didn't readily find a solution to: I bought six used 16GB DIMMs for my two Mac Pro 4,1's and a dual-Xeon server (running Linux). I also have some 8GB DIMMs and many 1GB and 2GB DIMMs. All are ECC. When I use the two 16 GB DIMMs, any other DIMMs are ignored. This is true in all three computers. I tried many permutations of DIMMs in slots on all three computers. Depending on the DIMM arrangement, I can end up with less than the 32 GB of the two DIMMs that are causing the problem....
I saw exactly this problem when a client bought a bunch of memory and installed it himself in a Mac Pro 1,1. I later got the computer back to install Linux and it showed minimal RAM, oddly, so I bought more. When I opened it to install the new RAM, I found it loaded with RAM that wasn't showing up. It took a while, but I eventually got the arrangement correct and all the RAM showed up.
(This, however, doesn't preclude the possibility that you just bought bad RAM.)