Regarding Marker, I'll file that and take a look to see if there is something off there.
Regarding FSE mode, it sounds like for some reason (perhaps a folder being accidentally marked read-only by the OS?) the settings file isn't able to save the changes you make. Can you take a look at X-Plane 11/Aircraft/***SR2X Folder In Use (SR20, SR22, SR22TN)/plugins/sr_systems/settings/settings.cfg
The line fse_override in that file sets the position of that switch. You can also go into the properties of that file by right clicking, and making sure it isn't set to "read-only"