@Ryu
I'm kinda in the same boat as you (I think ;-) )
I've got IDEfix installed, but don't use it. The only part I use is the atapi.device for the CD-Rom, which I have connected to the secondary IDE chain.
If I use the IDEfix that gets copied during the OS3.9 install, I get the register requestors (which my reg no does not work with) and I always get the "could not open atapi.device" requestor.
If I use the IDEfix that I got with the interface, I get a requestor saying "you need a new version of IDEfix" aswell as the "could not open atapi.device" requestor.
Removing the IDEfix line from the 3.9 startup solves the problem, and I have absolutely no bother using any hd or atapi CD-Rom on any position on the ide chains.
Another slight point...
After installing OS3.9 don't you still need to remove the "If EXISTS C:IDEFix" line from the startup? I think this gets added no matter what, so you'd actually need to remove IDEFix from C: to stop this, and not just comment it out on the pre-OS3.9 install startup.