A familiar scenario to me, as it has happened twice under similar circumstances b4 I twigged as to what was happening ie windows appears to be programmed to interpret 2 HDDs with the operating systems on the same computer as a fiendish attempt at piracy. The result is CMOS is scrambled and the offending HDD will never be recognised on that computer again.
First time I salvaged my data very carefully on another computer.
Second time I solved the problem with the help of "KILL CMOS" a freebie sometimes identified as a virus. (is not).
So, my advice is, disconnect the working HDD and chip away with "KILL CMOS" on a boot floppy. But first remove the CMOS battery and diconnect computer from power for half an hour prior to the attempt.
Good luck!
(You aren't paranoid? -PZ)