To be honest, I am starting to get the feeling there is nothing wrong and that it's our ears playing tricks somehow...
I just had both amps hooked up to a stereo cab with 2 G12-65s and I used an A/B box to be able to switch between both amps. Had the exact same settings on all knobs and started turning the tone knobs.
At first I thought I heard a difference in response of both Mid knobs but after playing for a while, I wasn't so sure anymore...
Thats a healthy conclusion you've reached. Our perception likes to play tricks on us.
Try to record your selfonce in a while. Its a good reality check on how you and your gear actually sounds.