If you have ANY mods active while playing the GAME MASTER scenario and you exit, your settings will get reset. Specifically the ones in ''Interface'', ''Gameplay'' and ''Game master''.
This exact same problem also happens if you ''LOAD'' a saved file/state from the menu at the top of the screen while any mods are Active
Sometimes it may even reset your settings/binds in the ''Controls'' section.
The first I noticed this was around the 1.6 version
I have also noticed that it wipes any mod presets you have created in the mod manager
REPLICATION
Enable ANY mod of your choosing in the MOD MANAGER
Start ANY GAME MASTER Scenario
EXIT or Load a save file
Check your settings
Settings should now be reset to their DEFAULT preset
WORKAROUND
CLOSE THE GAME WHILE THE SCENARIO IS OPENED
DO NOT EXIT GAME MASTER