How strange....the gain/peak have no affect on signal when amp is at 6 volume, but they do when it is lower 3 volume? Could this be some kind of impedance issue. I take it you have the correct jacks on Mutron plugged in (they are reversed from typical layout).
Never had problems on another amp, even at that high volume? There could be something wrong with the amp that is shooting down the line and screwing with the Mutron I imagine, but I am hardly an EEG. I would try the Normal channel on the amp, although they are not isolated fully on a Twin so the problem may persist.