ACC, fog lights and windows don't always work
 

2007 Mini Cooper S with automatic climate control. When you first turn the car, the climate control doesn't come on and windows/fog lights don't work. After between 5-20 minutes, it turns on and everything works fine until the car is shut off again. Seems like a sticking relay but I have no idea which as the labeling sucks. Anyone have this issue or know which relays/fuses are relevant?

Check your battery sound like it might me week and as such forcing the car to shut down some services like the AC/Heat etc. Then after it has had time to charge a bit it then allows the items to turn on.

I know this sounds crazy but the car WILL shut down items if there is not enough power to make them work. It is a compute controlled car you know.

I replaced the battery this afternoon, no change in the issue. The battery was 5 years old so no big deal to replace it as it was due, but that's apparently not the issue.

Well, I ordered a used climate control unit as I can't find a relay or fuse issue anywhere. Does anyone know if it needs to be coded to the car?

That module should just work for you. And I believe your diagnosis is spot on. Technically it is coded to the car, but as long as the same options are present it'll work!