Sounds like a weird one mate. I dont really have an answer that jumps out at me either. Just make sure that the ingame options are all set up how you want them to be and all that.
My only suggestion is.... (and only for a test) why not make that "settings.ini" file READ ONLY. You know, right click --> properties --> tick "Read Only".
See if that helps. It'll lock all your settings completely though. So it wont be a permanent fix, as all your kit selections ingame wont be remembered from game to game or night to night.
But as something to try before switching the read only OFF - it cant hurt. Might give you some indication if its just a settings issue or if its a software problem?
Hope you find an answer mate.