My room mate just had a problem almost EXACTLY like that with his Philips CDR drive. HIs drive would just sporatically disapear and XP would not find it anymore. This also was causing his other drive attached to the chain to disappear as well.
He fixed it with a firmware update from Philips.
My suggestion;
First, update to the latest BIOS available for your MotherBoard.
Second, find all the lastest firmwares for all your IDE CDROM drives and install them.
Third, get all the latest drivers for those devices (IDE controllers, MotherBoard, etc)
If that does not solve the problem, then we need to start considering a major incompatibility between your new MotherBoard and some of your IDE drives.
Keep us updated.
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