The only thing I can think of is a bad contact in the stomp switch, because it works when the effect is on proves there is a signal going into and leaving the stomp switch.
On bypass the contact should be closed on the top left terminal to the middle left terminal on the switch. (looking at the back of the pedal with the cover off)
The signal from the input goes to pin 1 of the terminal strip of the switch PCB, and then to pin1 on the switch itself.
The output signal goes through pin 6 of the switch PCB, and then to terminal 2 of the switch itself so there is nowhere to loose the signal except in the stomp switch itself.