There was no difference in booting. I tried with just 1 stick in, i tried with just 2 sticks in. I tried putting the sticks in difference places and occasionally couples with changing the graphics card and resetting the cmos, I would get it to boot up and be able to access the bios.
The 7-segment displays would sit at 20, 2A and 38 often. The screen would display the GUID error and 0033 from time to time. It wasn't predictable though.
When the system did boot to the bios, it did see all 6GB of ram and operated normally.
The boards being RMA'd to newegg as of right now. Hopefully that was at fault and not the RAM as I dont have any way of testing the DDR3 stuff.