I'm having the same issue. When I select a preset it activates and sounds as it should. when I turn off the "Active" button the effect turns off as it should but when I press the "Active" button again I get an almost inaudible amount of sound. I can just barely hear any output. I can tell that the effect is "on" but the volume is so low that it is effectively muted. If I change presets then the volume is back to normal. It does this regardless of what preset I change from/to and happens if its activated on the effect pedal, through midi, or through the app. Any ideas?

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 support@eventide.com.