I've done the sircam thing before. One tip - make sure you get it out of the recycle bin as well. A lot of AV proggies don't scan the recycled folder by default, and you have to get that with sircam.
Suggestion for an experiment - plug the CD-ROM in as a slave to your primary master HD. See if the problem continues. I'm wondering if Win2k is spending that time looking for a secondary master that doesn't exist, even though a secondary slave does.