|Are you SURE the Master/Slave settings are correct? Some Western Digital drives have a Master alone setting as well as a Master. Also, some drives have confusing labeling for the jumpers.|
While it is preferable to separate the drives there is no inherent reason they shouldn't work together. Has to either be the jumper settings or a defective cable.
You could also try using CS for both drives. When using CS, the drive connected to the end of the cable will be designated the Master.
Verify you are not reversing the cable either.
Are you using an 80 wire/ 40 pin cable?