Have you tried using a different tube in the V1 position in the amp? Wouldn't be my first guess, but I've seen tubes that have caused this kind of thing before. Maybe a little rare, but nowhere near unheard of. V1 is the most likely culprit, but I've seen power tubes do weird things like that, too, by throwing off the voltage to the other tubes just enough. But, as before, I don't have a schematic for your amp, so I can't be any more specific.
Other than that, the iso box would be my last suggestion before I'd recommend taking it to a qualified tech. It seems to me that a lot of the similar problems mentioned on this forum recently were related to something other than the pedal, but that's not to say that it's not the pedal, either. It could be, but without seeing it personally, I can't say for sure, and it could be a problem with the pickups or potentiometers, maybe even the jack in the guitar itself, or the settings on your amp, or more likely a combination of issues. It could be a bad solder joint on one of the jacks in the pedal, too.
I think the best that anyone can do, without having the gear on a test-bench, is to just suggest and try alternatives until, hopefully, something starts sounding better. I really do wish you luck with this… the TF is truly an amazing piece of kit.
