I’m using both a little disaster area midi pedal and a (TRS) three button footswitch — it wouldn’t be an issue (I’ve used the three button switch to toggle the tuner) but I’m now using the three button switch to control the looper.
You say you used the 3-button switch to toggle the tuner. Is it possible that one of the buttons of the 3-button switch was simultaneously mapped to switch to the next preset and toggle the tuner at the same time? I just tried it and it works. When I press the button, it goes into tuner mode. If I press it again, it ends up on the next preset.