Bump.
I have the same problem and it is very annoying. I ended up locking the settings for the Entrenchment file but now I have to reset all of the key bindings for regular Sins when I want to play that.
Where exactly are the Sins key binding files? Do Regular Sins and Entrenchment access the same file or different files? Why would Entrenchment have one set of key bindings but Regular Sins gives me only the default?