I think I know what you mean. I have the same problem with the mod factor. It goes to active, when bypassed, when you send a prg change. See this posting:
When you send a prg. change via MIDI. The modfactor changes to the program and activates it, eaven when it is in bypass. I think this behavior isn't right. The right way is, that the pedals keep its state, when receiving a programm change command via midi.
I've a time factor to and it behavies exaclty the oposite way.