The A4000's IDE is just a simple one: it simply expects a HDD to take a read or write command, nothing with a tape drive, CDROM, ZIP drive, etc. the extra instructions needed for these devices is in the software layer added by the ATAPI programs. They convert the control commands for non-HDD devices to work on the bus. More sophisticated IDE controllers have this in their firmware.
The fact that the HDD part of the controller works means that it is working at its basic level. The buffering may be affected, but I'm not able to tell you how to test it much less fix it. You could add a buffered device connector like they have for the A1200 and check it that way. I'm guessing that it is either something like that or you may need another ATAPI software program such as AsimWare's AmiCDFS Program (3.9 is the latest I've seen) to locate and configure the devices. There is also a difference in the IDEFix on Aminet and the full one on the Amiga Forever DVD that has the registration code -- I use the latter.
