In the Islander folder -> plugins -> is_systems -> settings -> settings.cfg, you can set "disable_persist = 1" to disable persistent settings.
Regarding the VFR transponder code, the way it is set up, if you are currently not squawking 1200 and click it, 1200 is set. If you are already squawking 1200, it cycles to 2000 (a common VFR code outside of the United States)