I'm having the same exact problem. Recently I built a PC. It was showing 6gigs like its supposed to but now its showing only 4gigs. The PC is one week old.
Windows 7 64-bit up to date.
ASUS P6X58D-E (BIOS Version 0303) second bios release and latest.
EVGA GTX480 (stock)
G.SKILL 6GB (3 x 2GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10666) at stock and shows as 1066 instead of 1333. I read thats normal. It is in the ASUS P6X58D-E list of acceptable RAM.
link to RAM: http://www.newegg.com/Product/Product.aspx?Item=N82E168...
I've been able to unplug the RAM and re-plug it and it shows 6GB again, but after a while it shows 4GB. That is after the second or third restart it shows 4GB.