Sorry, can't reproduce that?
After what action your settings are messed up?
I tried the following:
1) Set your settings
2) Closed the windows (right click)
3) Opened them again (all fine)
4) Saved the game
5) Loaded the game (all fine)
So sadly I can't reproduce that problem. Any steps on how to recreate that problem? Which RttR Version are you using?