The PF software is designed to run from the boot hd, not from floppy. If you don't install the software as outlined in my previous posts you will continue to go around in circles. The problem is not connected to OS3.1 vs OS3.9 but how the PF software works. Try to get into a position where OS3.9 boots properly from hd and has no PF software installed and you'll get there. Using floppies to run the PF software is your problem imo.
Cheers, JaX