Verify that each stick of RAM is firmly seated into the slot; the little clips on the board should close with a click when they engage the RAM.
Not sure about the BIOS HDD message, especially since it booted after POST. What is the HDD? SATA? PATA/IDE? If it's SATA is it plugged into the Intel Southbridge or the JMicron controller? See Pages 2-2 and 2-3 of your manual.
Alright, I booted up and got 6 Gigs of memory recognized, so I shut down again and tweaked the Dominators up to the recommended 1600 in BIOS (I7 defaults them to 1066), froze playing minesweeper, restarted, and am back at 4 Gigs.
Check these threads...There seems to be an issue with Asus Mobos and X58. All that is needed is some voltage tweaks, unless you have some bad RAM or Mobo. I was having the same issue with my Asus Rampage II Gene and it turned out that I had a bad stick of RAM. I tweaked a few things in the Bios from the below link and all my RAM was recognized.