Howdy Firewall,
I don't know how Commander works under the hood, but I think it looks in the same file data/Cfg/Flotillas.cfg (it's in the SH3 folder, not Commander)
Only when you use StartAtSea, it should be modifying that file to accommodate this.
Could you look at the above file, and compare your departurepoint lines to mine above? Not sure if reinstalling Cmndr will help, that's why I suggest this first
(I'm also in the 7th Flotilla/St.Naz. and have been starting in the pens)