If you are adding and removing mods through JSGME remember to roll back SH3 Commander beforehand, if you forget you can potentially screw your game. You probably know that already but I just thought I'd mention it just in case.
Sounds like you need to reinstall SH3 and your mods and start from scratch.
I'm running TDW's depth charge disturbance mod along with other mods and have had no problems with it so far.
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