Update: I went full retard on myself here .. I disabled the auto opening of the SRM and flipping to the right page. You can laugh at me now.
Only remaining question is regarding upgrades at gamestart .. after reloading the base save, and talking to the upgrade guy, he's selling a 10 cm deckgun .. if I buy that, it's not in game. I also have a second deckgun slot ... which I can put that new shiny gun in, but that still does not make it available on my sub.
All the other issues seemed to be user error
