Hi @sjdale, welcome to the GP community forum 
This could be because your controller send MIDI note messages rather than CC# messages. I guess this is something you can change in the software of your controller. Alternatively in GP, you could try to set your widget property in “momentary to latching” mode which is another way to solve the issue. Could you please tell us what is the message that you “MIDI learned” for this widget? If it is not a note message my assumption is wrong, then please, press and release your controller switch while monitoring what happens in the GP Global MIDI Monitor and post a screenshot of the result.
Having said that, be careful when bypassing an instrument plugin. It is safer to block note on MIDI messages, because if you play a note, bypass the plugin and release the note, it can be that the next time you unbypass the plugin you will ear a stuck note playing. But, I guess you are a guitarist trying to bypass an effect plugin rather than an instrument plugin.
Also, when you are more familiar with both GP and your controller, you could also have a look here: