Is the Auto-Load box checked in the Torpedo Management screen? If not, the crew will not load another eel into a tube unless you give the order to do so (manually drag and drop it into the desired tube).
Did you order silent running? If so, did you order the crew to stand down from silent running? Once silent running has been ordered, torpedoes will not be loaded even if you've selected Auto-Load as noted above. You must stand down from silent running first, otherwise - nada.
If you have Auto-Load checked and are not running silent when failure to reload occurs, do you have additional torpedoes available in the reserve slots, not including the external reserves? If you're down to external reserves, they cannot be loaded for firing until they are transferred to the inside of the boat. This must be done by the crew while you are surfaced, and you must order it by dragging and dropping the external eel into the appropriate internal reserve slot.
If none of the above "failure to load" culprits apply, then I got nothin'. I'm unfamiliar with some of the mods you're using, so can't speak to conflicts there.
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