All the pedals load into "active" mode. This is how the box works.

My copy of the MIDI spec (document version 96.1, second edition) does not specify the function of program change beyond, uh, changing programs, nor does it specify a bypass or active message as such. Sorry about that.

There clearly is an interest in being able to save programs in a bypassed state, and we will consider this for possible future updates. But, I would expect this to confuse as many people as it pleases.