@Josef
1. ERM from Reapers ui mod does not rescale the sil files to fit in the manual, so it need to be done manually.
Download this fix, includes the rescaled .sil files for these new ships. No need to load in bunker or anything fancy.
2. Are you referring to the new ships or any ships? At me, the ships sink much too slow and im using the same combo of fx+tiny as you do. Just last night I shot a blind salvo in a convoy and hit 1 ship in stern.. she just sailed away without any problem. Luck that luftwaffe joined the show so i had my revenge :P
But maybe you are good and managed to hit those ships right in their critical spot.
@Stormfly
Its a stock bug, happened with me once when a huge convoy spawned right over my head just when I was searching of a docked target. MN in stock campaign has all kinda weird bugs, was one of the reason I never managed to finish this campaign.. was a nightmare for me. But I will keep an eye on this issue and see what I can find...