Ok as for your tonnage issue, two things may of happened, Did you receive a Navigator Report in the speach dialog box in the botom center of you screen witch looked something like this:
XX:XX NA: She's going down!
If not then that would mean you did not sink her! If this did happen then when you were installing your mods, assuming you were using JSGME to do so, if you had any boxes coming up on mod install saying:
'"file.file" has already been altered by the "Example Mod" mod.
and if you did and clicked yes its more than likely you overwrited a important file to do with you ship sunk information and cuased it not to work. This may also be the case with you partrol not ending, of course it may be other things cuasing this but this is what i would of checked first. If it is a already altered file then just deactivate all mods and reinstall them again on JSGME, this time if that option box does appear just click no and dont install the mod!
I hope this has helped,
Jonny
Sorry for spelling mistakes and grammer!