While voltage is consistent on all USB ports, it is possible that amperage is not nearly enough to power the circuit for complete read/write. That would cause the drive to fail its own POST and refuse to send the proper signals to OS 9. It's pure speculation on my part, but you can troubleshoot this part of the circuit by plugging the USB floppy drive into a powered hub with 500mA minimum. 1A is better, but harder to find.
I had success using a floppy drive connected to USB on a G3 iBook. The thing would only work when connected directly through the ports on the machine. When I used the G4 PowerBook, it wouldn't work and I had to move it to a powered hub. Early USB 1.1 devices tended to not think of the future of powered devices and were intended to only charge the circuits of mouses and keyboards. 350mA was plenty for the time. Even USB 2.0 had no interests in much more than what a flash based hard drive could do.
Again, this is only anecdotal evidence. YMMV. Good luck!