First checck your cabling. You should be using an 80-conductor IDE cable (with thin-looking conductors, not the older thick type). It should be up to 18" long. If both drives support cable select, you should try that first, not manual master/slave configuration. If cable select doesn't work, you can do it manually by jumpers, but put the master at the end of the cable and the slave in the middle of the cable. If you still have problems, try swapping the master/slave positions of the drives, and also try another cable.
You didn't specify your operating system, but assuming you are using Windows 2000 or XP, go to control panel and the IDE controller settings and make sure both drives are set for DMA access, not PIO access.