Are you using the preamp signal from the dual rec fx send and running that into the board, or are you going guitar-board-fx return on amp?
Since the fx return is after the preamp in the signal path, you will bypass those controls if youre not plugging the guitar into the amp and coming out of the fx send.
Nevermind, I figured out the issue. I thought that the Boss Line Selector pedal would send constant signal through the in/out and that engaging the footswitch would just turn on/off the loop sections. It doesn't work like that. When you turn on the loop it stops the signal to the front of the amp. Basically, I thought they would work in parallel. That is what I get for listening to a guitar store salesman.