I had a similar problem...
In my configuration, I had three HD's and one CD-RW, with the CD-RW set as the secondary slave drive.
XP would see the CD for a short while after boot-up, but within less than an hour, the CD would disappear from the system altogether. The only way I could get it back was to reboot.
Then I added another HD, and a DVD-ROM and had to add another IDE controller card.
I shuffled things around so the CD-RW was set as secondary master, and the DVD as secondary slave, with the HD's set as primary slave/master and the remaining HD's on the add-on controller. I haven't had any problems with it since.
Somewhere along the line, I read an article about XP and some controller/drive combinations. I can't recall the exact details, but the gist of it was that XP frequently doesn't like an IDE drive and an ATAPI drive on the same channel, so try moving the CD off of the IDE channel containing the HD and see if that helps