If it has an effects send and return, put a patch cable between them and see if that fixes it. If it does, it's dirty jacks. A little Deoxit on a plug pulled in and out a few times should fix it. Also, a dirty headphone jack can cause this.
I think where you're at is the pre to amp interface. And normally that would be a good thing to try. However we have enough info to point in another direction this time.
The same problem occurred with two different amps, one was brand new. I think the problem is post amp.