My suggestion:
Set the Behringer switch program change (one of 5 per-switch) to the same MIDI channel as your amplifier. For example, FCB-1010 sending, & your amplifier receiving, on MIDI Channel 1.
Program your FCB-1010 expression pedals and set the TimeFactor to another MIDI Channel. For example, the FCB-1010 pedals sending, and the TimeFactor receiving, on MIDI Channel 2.
Leave the TimeFactor OUTPUT = THRU. While the CC messages will still pass through the 'Factor pedal, your amplifier won't "see" them. The FCB-1010 MIDI Channel programming happens under Global Configuration.
I hope that I'm understanding your routing chain. If you're using the TimeFactor as a master MIDI Clock, you may have to place it before the FCB-1010, and set the pedalboard to MIDI Merge option [Global Configuration – Config page].
