Here's how I do it on all the JRs I have owned.

I'm going to assume you have a Flaperon wing type set. If not go to the System Set-up Menu and set it.

1, clear all your sub trims and end points and center trims.

2, Put the control horns on the servos so they are centered as closely as possible.

3, Hook up ailerons and center as closely as possible manually using the clevices or pushrod connectors.

4, Use sub trim for flap and aileron to center each side.

5, Go to the Elevator-Flap mix and set both directions to 100%. You can change this later, but set 100% now.

6, Put Elevator Mix switch on so the flaperons work. Hold full up elevator, this should give you full down flaperons. Position the plane upside down so you can see how far both flaps went down. Use Travel Adjust to reduce the greater side so both are exactly the same. This will need either the flap channel or the aileron channel to be adjusted. Once this extreme position is adjusted, the intermediate positions between center and full will be fine.

7, Hold full down elevator for up flaperons and position the plane right side up so you can see both flaps and reduce the greater so both are the same.

Now when you have flaperons on and do a full up loop or land with flaperons, your plane won't roll. You can now reduce the flaperon travel or not even use flaperons.

I like to set every plane up this way using flaperons whether it is a fun fly plane, a sport plane or a scale plane because I can adjust each side individually.

What's probably happened to you if you have the pushrods in corresponding holes is you have a minot thickness difference in horn length due to tightening one side more, reducing height or maybe one horn isn't exactly over the hinge line. There are always some slight differences in servos, too. This is the reason the big guys need things like the Match Box.