In the Submarine folder, the EQP file, which is text-based, and the SIM file, which gets opened in S3ditor. Look under the "wpn_SubTorpedoSys" nodes. It's basically the tubes on the boat, not the torps themselves. How are you doing your "fresh" installs mark bonamer? It's almost like there's a little something in your installs that shows it's face when you apply a mod. In other words, what's the source of your files, the path to the game, the version of JSGME, etc.?
I probably didn't state it very well, but I was referring to your getting the Mark 14 torps in your S boat possibly being caused by the mod change during the career. If you did empty the Save folder, and started a new career, then I say (again): "I dunno"... Very strange - though years ago, not so strange. There used to be all sorts of weird nigglies in the game. My original disk was almost unplayable from a career perspective, unless of course, you died after a couple-three patrols. Otherwise,
something would bomb on you. Ubi kept throwing "updates" at the game, which sometimes broke more than they fixed...
My brain is remembering a post on here (maybe the Ubi forum??) about someone having found an issue with the torps, but I'm thinking it was pre-v1.4 release - and it may have been SH3... then again, I are old, and I've slept quite a bit since 2007, including those afternoon naps on the couch, where I don't even remember having had lunch when I awaken...

- maybe some one of the old heads here can remember that far back...