Sounds like you might want to try a different pedal.
You could use a normal resistive pedal with a 3 way Y-lead as long as this will not create ground loops.
Also, there may be issues with MIDI thru. Temporarily connect each Factor in turn directly to the pedal and see if you have the same problems.
The Factor pedals have a 5% margin for heel and toe detection, so you only need to be close to 0, not actually hit it.
You would probably be wise not to use a MIDI pedal for very fast sweeping – there is always a bit of "rubberiness."
