Sorry. We cannot duplicate these problems, so it's hard for us to respond meaningfully.
As soon as I updated the pedals to version 3.5
Did you re-init the pedal before restarting FactorLib ? Worth a try.
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.
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.