Sometimes I face the same problem with my H9. And also using shimmer.
It´s like it freezes receiving the signal and keeps sustaining it in a very high signal input. When it happens, I have to restart the pedal, because if I bypass it, it stops, but when activates ir again, the crazy thunder sounds are still there.
I have no clue about what it could be. The signal path is guitar -> pod hd pro -> (dry out) -> H9 -> mixer -> amp.