On Sohcrates suggestion...
---if you can only remove the parent device from the device manager, if you want to remove the primary and secondary controllers, run regedit, goto the branch "HKEY_LOCAL_MACHINE\Enum\MF" and delete the appropriate 2 branches
Some possibilities:
-this first possibility is one I recently saw, when installing a new 20gb WD drive, so I suggest this one first.
---after trying about a dozen things, I open up the case, look at the jumpers, they were correct, and it looked like it should have worked without any problems(I guess the motherboard/win98/drive didn't like it no matter how correct it looked), but I had nothing left to try, so I tried each jumper setting, and then boot into windows. One of them took the drive out of compatibility mode and removed the exclamation mark from the ide controller it was on.
some more farfetched possibilities...
-it was drive overlay software was it (then it might have added a .386 file that loads on bootup, this can cause it)
---remove it the line that loads it from the system.ini and restart the system
-ide controllers just got a little confused and disabled 32 bit transfers
---goto this branch of the registry "HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\VxD\IOS", if there's an item named "noide", delete it and restart the system.
-ide controllers+windows are extremely confused and IOS.LOG in C:\windows reports a "ESDI head mismatch"
---either a drive is bad, doesn't like the master/slave settings it's on, or the primary/secondardy channel it's on, or the other ide device that it is sitting with.
---only way to confirm is to do a fresh format and reinstall and see if the IDE controllers+IDE devices are just as unhappy.