I know this post is a little bit old, but It's the only one I found that has the same problem that I.
In my case, I have a Line 6 Spider IV 120w and have the same problem. It begans with uncontrolable channel volume Knob, then I reinstalled firmware and did factory reset but the problem now is that the Treble Knob is controlling Volume Knob. Any Idea how to Fix it?