I have recently ran into this problem, while before, everything worked fine. The CD drive, a Samsung SC-148F, is jumpered to be in the master position, and the ZIP drive is positioned to be the slave drive. No "cable select," here, I always find that cable select is finnicky and I haven't used it in years. Both drives are on the same IDE cable, with the CD drive using the upper connector, and the ZIP drive using the lower connector.

Data transmission rates seem to be significantly reduced when the ZIP drive is plugged into the same cable with both power and IDE. When only the IDE cable is connected (no power cable), the attached CD drive will not function at all, or even power up. When the ZIP drive is fully connected, the data sent between the motherboard and CD is also unstable and erratic, causing the CD drive to have physical issues with the speed at which the disc should spin (it will spin up fast and slow down, and repeat this), and how to move the laser itself (the laser will erratically move based on what I can hear from it, as if it's trying to read a badly damaged CD).

This has caused crashes in Windows 98 FE and SE setup, and makes booting from any CDs, especially Hiren's Boot CD 15.2, incredibly slow.

This was not a problem when I still had the original Windows 98 SE installation from the previous motherboard installed on the hard drive. I also have entered the BIOS to try and optimize a few settings, but I don't remember messing with the IDE options too much. Everything has been left to "auto," if I remember correctly. I will check the BIOS after posting this to see if any settings strike out to me that may relate to what's going on.

[EDIT]

Apparently "'ol reliable," is reliable no more- thing is dying. Replaced it with a DVD-ROM, everything seems to work okay now, plus my system can read DVDs now, for what that's worth.

Had nothing to do with the ZIP drive, you could have the thing alone, without even the HDD connected, and it would get ornery. It took me tons of testing with various configurations and different CD drives to figure it out. I may be able to clean the laser on the drive, but that's all I can really think of that might fix it.