Darock:

IMHO you are on the right track.

It is very likely that he set up his linkages with the servos not centered.

The JR radios permit you to save trim settings which become the default "zero" point if not cleared when transitioning or setting up a new plane.

In this case I'll bet that he does not actually have the servos at their zero point and has compensated by turning the arms so that they LOOK like they are equal.

This creates exactly the condition he is discribing, namely that all the linkages and throws and settings are correct but you end up with more travel in one direction over another.

Subtrim should also be looked at in the radio.