I've had a similar problem myself, though when installing a cdrw drive into my existing machine, the only way I could get it recognised was by installing it on the primary IDE channel as the master device with the hard drive set as its slave.
The secondary channel has the DVD drive as master and internal zip as slave.
I know this is not the accepted way of wiring things up, but for some reason it's the only configuration that works in my set up.
If I place the cdrw as slave on the primary channel, or as master or slave on the secondary channel it just isn't recognised. BTW It's a RicohMP7200A drive, and Western Digital caviar hard drive.