Moving the sticks around doesn't do anything unless an application is "looking at" them. Either FPV Freerider or jstest-gtk needs to be running in order to recenter the sticks. This is what I have been doing. Move the sticks around and then close and (re)start FPV Freerider.
If I run jstest-gtk first and move the sticks around, then run FPV Freerider, it initializes just fine, but that isn't really a true fix. As long as something initializes the transmitter before running Freerider it works just fine.
The first time I start FPV Freerider with a transmitter I have just plugged in, everything is off center. Then if I close out and restart, everything centers perfectly. This happens with both of my transmitters. It only happens in the Linux version of FPV Freerider and Recharged.