Just read through all the suggestions here, and this is like deja-vu from when I had this problem with a Rampage II Extreme board.. I had just transferred an i7 920 C0 and 6GB DDR3-1600 from a vanilla P6T where everything was verified as working properly. Once installed in the R2F board, I noticed the OS only had 4088MB RAM available, while CPU-Z reported 6GB.. while I had another 3 slots to try, it was recommended in the manual to populate the primary bank first for best performance, so I decided against this "workaround" and contacted the manufacturer. After a brief conversation with ASUS Live Tech, it was verified that I had done everything to make sure the BIOS was up to date, and everything installed correctly, and even re-verified in the P6T as still-working, the ASUS tech granted an RMA request.. The board I got in return worked flawlessly and counted all 6GB RAM, and was also available to the OS.
I have recommended this solution to more people than I feel comfortable with at this point.. It seems to be a very common issue with ASUS X58 boards, and is likely due to some disconnect between the DRAM slots and the CPU socket, which you will not be able to resolve.
I wish I had a simpler solution or better news, but I believe the only way to resolve this issue is to RMA the board.. Since it's a GENE, it should be covered under the free advanced RMA program available to Republic of Gamers product owners, so bring that up in the RMA request also.
Oh, PS. If the ASUS tech tries to tell you that your components aren't QVL and you should replace them, just tell them you verified that everything works on another ASUS X58 motherboard.