So to recap - 2 drives (both with operating systems?), machine working fine until yesterday with both drives connected.
You do nothing (no changes to software/hardware etc?), then today machine just makes a noise and then shuts down if both drives are connected. But machine is ok with each drive connected separately.
Very strange. If this really is the full story, its hard to give any advice, as you appear to have 2 working drives and a working machine, and no changes which could have caused the problem.
Run chkdsk (or scandisk if win9x/ME)? Run drive manufacturer's diagnostics? Swap the drives round (master/slave reversal, put one on secondary IDE with CD/DVD as slave...)