I take this to mean that you've jumpered your drives Cable Select. What for? Assuming you're using a standard (P)ATA cable, jumpering your HDD to Master and your DVD drive to Slave ought to be all that's needed. To be able to make use of the Cable Select feature you require a special data cable where the pin 28 signal is routed to the middle connector only (pin 28 must be open at the second connector).
Now, chiming in with a VERY stupid question: Did you even try to jumper your HDD to Master and your DVD drive to Slave?
And oh, BTW, for good measure I'd recommend connecting your HDD to the connector at the end of the data cable and your DVD drive to the connector in the middle.