Hi. See this link for your problem I think:
http://www.subsim.com/radioroom/show...8&postcount=10
Additionally, I'm assuming you started with the 7th Flotilla. Often a conflict of the bases occurs with the 7th through August 1939 in the flotilla.cfg. A lot of people recommend you just transfer to another flotilla at this time to avoid this issue, but I fixed mine when I needed to by altering the file with non-conflicting dates.
To avoid issues regarding 7th flotilla base changes in 1939, copy/paste the following over the relevant text in flotilla.cfg. (Be sure to back up your old one first in case I'm wrong).
Flotilla2=904
TO2=940
NbStartingDate2=7
NbDate2=7
Emblem2=data/Emblems/SubEmblems/Flotillas/7th flotilla.tga
NbBases2=4
Base2_0=765;Königsberg
Date2_0_0=1939
Month2_0_0=7
Date2_0_1=1939
Month2_0_1=8
DeparturePointLong2_0=2446551.000000
DeparturePointLat2_0=6560480.000000
Heading2_0=335.051331
Base2_1=750;Kiel
Date2_1_0=1939
Month2_1_0=9
Date2_1_1=1940
Month2_1_1=8
No guarantees this will fix your problem, but I think with these two bits of info you should be getting close. Probably a good idea to restart your career too to avoid corruption. Good luck.