As Fincuan says, part of your problem is fixed with the 1.4 patch.
If you have enabled mods and try to load a saved game (one that doesn't start in port) it will crash. Once a mod is enabled you must start "fresh" from port, you cannot start mid-patrol.
I would disable your mods, install patch 1.4 and restart that particular mission from port (assuming you still have the game saved at that point). Do NOT install any mods with patch 1.4 unless they are recognized as being compatible or you run the risk of continuing problems.
It's frustrating I know but you're not the first to experience this.
