Step 1 add missiles to a tech light class frigate as a template for an alternate race.
Step 2 load the game, missiles fire perfect cannons fire perfect.
Step 3 Save game.
Step 4 Go to main menu load the save game.
Step 5 The only weapons that fire are the tech cannon.
It seems like some how it's reverting back to the original tech frigate some how on load. It's not like in the beta era either where you could just look at the save game file and see what's been changed.
I've even tried the decryption and that doesn't work so i have no clue to what's going on.