Well, I think the starting spot is controlled by a long/lat setting given for a particular named location in the game... the start at sea option just alters it for the bases in whatever file that info is in, so the "dot" on the map for Kiel or Willy or whatever is moved and the game places you there instead of inside the harbor when you start a patrol.
I don't have access to the game files ATM, but if somebody knows which file contains that info you can check and see what the current long/lat settings are for the different bases, or maybe find another mod that's done something with that particular file and see if that's the source of the alternate info that's placing your base outside the harbor.
If "start at sea" is
unchecked in Commander, I assume it wouldn't be making any changes to that info when you launch the game... so whatever is there already would be controlling your start position. The settings for the base's location on the map have gotten changed somehow, it sounds like, and Commander's not going to mess with them either way if you're
not telling it to start you at sea, cuz it has no reason to touch them at all. Even if you did check 'start at sea' for one patrol, and then rolled back, it would just roll back to what was already there before you started that session, which is apparently placing your base outside the harbor anyway.
Seems like the simplest solution would be to find out what the original locations settings are for the bases and make sure they are in the proper spot in the game files before you start the next patrol. Then if you don't tell Commander to change them, and another mod is not altering that file after you make the corrections, the game should locate the bases back in their usual positions inside the harbors at the subpens.
