Hi,
I also dock the u-boat, but always in any pen or dock OTHER than the one i started from (stern first of course!). This is to miss the bug - that when returning from a mission in campaign mode, if you get too close to the starting point of a mission (dock)... you will not recieve any credit for anything you accomplished and you will not be awarded any points.
See Community manual for above:
http://www.communitymanuals.com/shii...tle=Known_bugs
Kaleun