On the calibration screen of FPV Freerider, are you able to move any of the little circles up and down with the left stick?
If not, you might be able to remap the output (in the menu of the transmitter itself) so that it send to another channel.
If you are able to move them, but the problem is that the automatic stick detection selects the wrong channel, you can just click on the little circle that you see is the correct one for the stick that you are currently calibrating (instead of just clicking OK).