One important thing I've learned about the ToneX App is that you have to watch out for dual processing, since the pedal is also an audio interface.
If you are using it in Librarian mode only, to manage the sounds on the pedal and playing through it, turn off the Input in the app settings. No audio should be going through the app at all.
If you are playing through the app, using the Tone Models there, you need to put the pedal in Stomp mode and bypass it, so it's not processing the audio as well.
They could improve the app by making this automatic, I think: mute input when on the Librarian page, and bypass the pedal processing when on the Home page playing through Tone Models there.