Have just installed the Utility V1.6.1 and used it to update to V3 software successfully for my TIMEFACTOR and works a treat, however exactly the same process for the MODFACTOR and the utility does not recognize / cannot find the pedal. Have tried everything I can think of and scoured from the tips here. Both pedals were bought on the same day and used in tandem ever since with no issues.
What version is currently on your MF? I'm guessing you have MIDI CLK OUT turned OFF… What type/OS computer are you using? Have you tried placing the MF in update mode manually? I'll guess you're using the same USB cable that you had success with on the TF. Have you tried connecting the pedal, then turning off both the pedal & computer, wait 5 seconds, turn the pedal on, then reboot the computer? Do you have any other USB devices hooked up at the same time (if so, have you tried disconnecting everything but the pedal)?
Anyway, just a couple of thoughts there… any details you can provide about your OS and what you have tried might help us figure out what's going on. I'm sure there's a solution… Good luck and keep us posted, ok?