I've seen a post somewhere around here regarding this issue. What I suggest you to do is to reinstall the game. Do the clean install than patch it up with 1.4b and than install GW. I strongly suggest you to use the mod enabler for installing any modes.
When it comes down to the loading the torps... well one of the files that contains the settings with efficiency for the torpedo room is corrupt and the minimum efficiency setting for operating the torpedo room is changed to much higher than it should be. That’s why you cant reload torpedoes even having full squad working on them. I had the same issue after clean install i did not have any problems with it.
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