There's a status bar above each compartment where work can be done. Those bars represent the work state of the crew in each compartment. If the crew is too tired or you have too few crew in there, they won't load anything. Nothing will also be loaded if you set the sub to silent running. Also, make sure that Auto-Loading is unchecked on the "Weapons Management" screen. I will suspect you have one of these problems. I play SHIII with GWX 2.1 all the time and have had no problems with torpedo loading ever.
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