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Could you try resetting the H9s system settings and disconnecting everything so its just a guitar, the H9 and an amp to see if this still happens?
Someone mentioned above in this thread that this is happening when changing presets from Ableton. If you could zip up an Ableton session and send it to us and let us know what H9 presets you were loading (maybe export the H9 preset list), we could have one of our testers try to reproduce the problem here. You’d just need to send the session to firstname.lastname@example.org.
I am not using Ableton. Sorry for the miscommunication. I am using a midi footpedal to change presets and have tried disconnecting from all other equipment and running guiter>h9>amp but still getting the same issue. I’ll try a factory restore and see if that helps.