***ALERT***
STOCK SH3 KNOWN ISSUE WHICH IS HARD CODED AND CANNOT BE ADDRESSED BY MODS:
Stock Silent Hunter III has a hard coded issue that has been experienced since date of release that occurs when a player leaves port, goes out on patrol, sinks targets and then returns too close to the original starting location in port which results in all "points" for the mission being discarded. your modifications have not caused this.
this known issue does not occur all the time and appears to be random in its nature... so dock at your starting point at your own risk! The only suspected way to fix it would be for Ubisoft to release their source codes/ SDK which is not likely to happen.
Fix: for now, the only known fix is to avoid returning to the exact starting location in the port from which you originated. (ie. dont drive the sub into the dock by the cheering crowds) - instead, maneuiver your boat to another section of the port OR close to within 10 - 20 KM of the home port and hit ESC then select the "DOCK AT" option to end the mission.