I could be entirely wrong here, but it's possible you are confusing yourself. I would suggest that you first "Restore Factory System Settings" (see UM).
Then, set the Levels switches to the same positions and keep them there (preferably Guitar, only Line if this distorts).
At this point, the output level should be much the same as the input level. Confirm this by seeing if the level changes much when in RELAY bypass.
Then leave the level settings alone and see what happens.
It is unlikely for the TF to change its levels spontaneously – consider that the problem could be caused by other equipment. If you still have the problem, try Guitar -> TF -> amp and see what happens.
