Just run the calibration procedure (don’t forget to patch a dummy cable in the FM input!). It looks like the module hasn’t “learnt” the right offset for the FM input. Probably from an earlier calibration procedure not performed correctly?
Yes, it’s due to a different in signal path when using the sympathetic strings mode with an internal exciter. In this particular configuration, there’s one normal KS plucked string (whose damping is controlled by the knob), fed into the sympathetic strings (with a default damping value).
When the internal exciter is not used, the damping knob controls the damping of the sympathetic strings.