Pripley, Based on what you are saying, it sounds like the issue you are running into is due to the dimms you are populating the server with, which sound like they are UDimms. With Udimms, as well as Quad Ranked Dimms,  you are limited to 2 Dimms per channel. On the bottom of page 129 of this manual you can see this limitation.  Let me know if this answers your question on the memory issue, or if you have Rdimms and are seeing this. 
I have an issue that has me running in circles. I am populating a PE R710 server with 1GB 1Rx8 PC3-10600E DIMMs, which works fine when the first two DIMM slots are populated for each channel. However, when I populate the third DIMM slot in any channel, I get the E2011 Memory Configuration Error.  I have already updated the system board BIOS to version 6.4 and am still getting this error. Can anyone out there tell me how to correct this? Thanks!
PowerEdge R710 E2011 memory configuration error