Were the drives working correctly with CDs before the re-format?
Are the drives being correctly ID'd by the BIOS? It's possible that in the past the BIOS has not been set for this and Windows has been IDing the CD drives itself and ignoring the BIOS. (In fact in some installations the BIOS is deliberately set to NONE for optical drives, as the BIOS equipment table passed some wrong information to Windows.) If the drive ID options are set to AUTO, try changing them manually to CDROM, or vice-versa, sometimes one way works better with some drives.
As far as booting goes, the BIOS could perhaps be confused by the presence of two CD drives, and may flip into action if only one of the drives is connected (assuming they are IDE drives, with the drive on its own channel as Master).
Edited by Platypus, 28 December 2008 - 05:19 AM.