
Did you previously install and use the non-Store edition of FileBot by any chance?

The Microsoft Store APPX application sandbox will isolate each and every Store application, but will maybe try to use existing
%APP_DATA% folders and registry entries, so things could go awry there.

You can try running
filebot -clear-prefs to see if that makes a difference. Alternatively, deleting the
HKEY_LOCAL_MACHINE\SOFTWARE\JavaSoft\Prefs node via
regedit can also help reset things completely.
UPDATE:
Newer versions of Microsoft Store edition will store your user settings to
%USERPROFILE%\AppData\Local\Packages\PointPlanck.FileBot_*\LocalCache\Roaming\FileBot\settings.properties on close.
If you open 2 FileBot instances open at same time (thank you for providing a screenshot that shows 2 FileBot windows open at the same time) then each will overwrite the
settings.properties file on close, so the settings which are saved are the settings of whichever FileBot instance you close last, and each FileBot instance is only aware of settings at startup, and will not be aware of any settings you set in other FileBot instances that are running in parallel.

The solution is to only use
one FileBot instance at any given time.