You would be better off having your IDE configuration like this:
Hard drive 1 (master)
Hard drive 2 (master)
CD burner (slave)
The CD drive positions can be swapped over, depending what hard drive you tend to burn from the most. The idea is to have the most...
Possibly shortcuts from files on the CDs that Windows is trying to refresh. I've seen this happen a lot with files on floppy that people have saved, and then Windows tries to reaffirm the shortcuts every so often and the floppy drive goes mad.
Also, it wont help if the CD drives are connected...