I don't think you understand what I do understand... Rough seas, torpedoes run deep... When a torpedo is initially launched, it will drop in depth until it gets up to speed, then the depth control will attempt to regulate. But in addition, notice how ships ride in the ocean? They kind of "bounce" up and down with the waves. Notice how torpedoes "ply" the waves? They kind of bounce up and down as they try to maintain depth. Notice torpedoes run deep due to BdU failure? Notice that the magnetic pistol fails? Not a good combination. Read the articles at those links above for more. Those issues are modeled in most mods, as well as the Stock game. You just might not be able to attack in rough seas. Have you used the external camera to try to follow a torpedo to a target, and verify how they run?
Now, part 2 of the problem could well be your mod activation, if using any. Be certain you followed all instructions concerning any mods used. If you are not too far into a career, empty the Save folder ("C:\Users \UserName \Documents \SH3" by default), and try to do a new career. That will create a new Save data structure next running of the game. Any leftovers from Stock or other mods that might have been in the Save folder can cause issues. Any added mods that are not compatible with the mod currently used can cause issues. Any mods added or removed after you start a career can cause issue. Shelling out to Windows while playing the game can cause troubles. Most things being computer-dependent.
You report a problem, but have not fully described it. If you still have issues, post back with your mod list, a description of your targeting procedures and pictures if possible. Right now, this is kind of like throwing darts while blindfolded, without more info...
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