I'm sorry to hear that you are having issues with your memory upgrade.
I can see that you are able to get the system to see and use the full 16GB by moving all the memory to one riser, is that correct?
If so your system is detecting the memory and it's working fine. Mac Pro systems are very particular about how to put the memory in the system. If you have found that the system will work fine with 16GB in one riser than it's perfectly fine to run the system that way.