Sorry. We cannot duplicate these problems, so it's hard for us to respond meaningfully.

jb4674:

As soon as I updated the pedals to version 3.5

Did you re-init the pedal before restarting FactorLib ? Worth a try.

jb4674:

I have noticed that there are 4 files within the FactorLib directory corresponding to each factor

These are the factory presets at the time FL was released, so it can be used off-line.

jb4674:

what type of USB driver is being used

The 'Factors use a class-compliant MIDI driver that is a part of the OS on both Mac and Windows. If for some reason it was corrupted, it would probably require the OS to be re-installed. You might want to try uninstalling the pedal and reconnecting it.