I have this problem on my Windows 7 desktop PC at home, that from time to time my secondary 1.5TB WD Caviar Green hard drive disappears from the system, as if it wasn't installed at all.
It turns out to be a bug in how Windows wakes up SATA drives--there is a time-out, and apparently some large SATA drives don't wake up fast enough, and are assumed to be missing.
There is a Microsoft hotfix for the problem here.
If your large SATA drive isn't the primary drive, then you won't see the BSOD or error messages, obviously. Instead it will just be disappearing.
