Okay just to update,
I uninstalled everything SH4 related this morning, and did a fresh install, with no other mods than OM and this time i put the Hotfix on it, and tested sinking a few ships etc. and all works fine now. fired 1 torpedo at a small merchant and it sank after about 15minutes, so they take a while to sink (which in my opinion is alot more realistic) but at least they finally sink now
thanks for your help guys,
Cheers.