Zandronum

having an issue were when I exit the game all the controls revert back to defaults. I tried to set them again and they don't save when I exit the game and enter a new game. Any ideas?

That sounds like you have Zandronum installed in your Program Files folder. Programs that write to their own folder, which used to be the standard way to do things, don't work well in Program Folders now that modern versions of Windows write-protects Program Files. To fix the problem, move or reinstall Zandronum outside of Program Files.

run as administrator

Making scripts to bind all the the keys to the their corresponding designated actions and calling them to execute from console is one way.
For instance make exec main.ini where ini contains everything set up.