are you sure you reconnected the CDROM drive to the same IDE connector it was connected to before? i mean primary/secondary channel, master/slave position.
since there are 2 hard drives this leaves only 2 possibilities for the CDROM. maybe try to move it from the one it is on now the the other one that is free. maybe that's what's causing the problem ?
(wild guess here, but can't hurt to try, definitely much less work than reformatting the HD and reinstalling the OS).
One Ring to rule them all, One Ring to find them,
One Ring to bring them all and in the darkness bind them
In the land of Mordor, where the Shadows lie
M.C. Escher - Reptilien