Nothing is wrong.
As you have a PRO version, simply record enable the guitar channel (in the “RECORDING” section above the Performer Monitor Mixer) and use “Get HD Files” after recording. This will create a new mono track with the full resolution Performer recording. You may then choose to delete the stereo track.
The signal recorded in realtime is always stereo. Alternatively, you may hard pan the two channels left/right (again, in the RECORD section) and split the stereo file after recording, this can also be done with the SE version.