I’m going to take a wild stab at this; no doubt you have already eliminated the usual suspects. But I noticed having similar aux switch / looper issues at the start. Turns out the parameters were triggering on (momentary switch) release. Aux switches that I’ve always used elsewhere; never adjusted the options (intentionally). I use a pair of Boss FS-6s. Flipped the polarity switches, and that’s what it was. Momentary on switch press. I’m not projecting that as your issue there. Something I ran into myself.
An interesting observation. I don’t think it’s causing my issue, though, because I’m having the same problem with the onboard switches. Calibrating the aux switch also shows the appropriate triggers lighting up on press, not release.