Is there an answer to this yet? I'm having a similar issue with mine using a Western Digital Red WD10JFCX drive. I thought that maybe it was just the drive so I hooked a 500GB Seagate Momentus XT drive up to see what happens. Both drives seem to show up during boot every now and then, and sometimes they don't show at all. When they do show up and stick around for a while in windows (Win 7 64 bit), they just stop working and disappear after a while. If I hook these drives up to an external enclosure and plug them in via USB port, they seem to stay working.
This is very annoying. I've updated to the latest BIOS version to see if that would fix it, and it didn't.