Hummm, okay. You mentioned before you were able to boot to Workbench normally with a floppy disk, correct? Try booting off your HD, but hold down both mouse buttons and do "No Startup-Sequence". Then put the floppy disk in the drive and try running just the SetPatch off the floppy disk (cd to DF0:C directory). Does that work? What version is on the disk?
What version of the OS were you booting off with this disk, BTW?