This has happened to me 2 times today and I think one time last night, and I don't know why.
I have my 640GB HDD which has my OS partition, and I have my 1TB WD HDD which has games and other things. For some reason that hard drive and both partitions disappears from windows. Rebooting fixes it, but I don't want to have to do that who knows how many times a day.
EDIT: I Think it was a prob with my sata cord. I moved it and plunged it into a diff sata slot and I changed my power management and it is still going ok...so prob solved!?