Have a look at the cfg files in data/subamarine/YOUR SUB
Check to see what the values of the "stormconditions" modifier is set to. If it is set to 7 and .1 then that is the original value and this isn't the problem. If those numbers are higher then I think this is your problem.
I have altered these numbers manualy so I can use the flak gun in bad weather. After I did this, my crew didn't wear wet weather gear in the rain. It's a price I'm willing to pay for some air defence :|\
________
HOW TO ROLL A JOINT