A huge number of variables in your summation, but, even though I'm a Vista sceptic I wouldn't blame it just yet.
If the bios couldn't find the drive, there is definitely something going on. You've changed sata cables - was the power cable seated properly, and is it using any 'splitter' cables that aren't seated correctly?
If you are confident that all is fine in the cables department, I'd really be questioning the reliability of the drive itself. Most drive manufacturer's offer a test app on their websites. Try that - but run the full test at least four times. When I've used them they seem to sail through, until they are hot. Then the app finally puts it's hands up and says 'dead'.
Maxtor anyone?