This problem is caused by the availability dates stored in the stock SH3 Basic.cfg file (and carried through by Grey Wolves) and will occur if the SH3Cmdr "Correct U-boat availability dates" option is not selected.
The stock availability dates for the VIIB and IXB are set to 10/39 instead of 9/39 and hence will not appear in SH3Cmdr before 10/39.
To fix, you can do one of three things:
-Start all new careers in SH3Cmdr with the "Correct U-boat availability dates" option selected. Before running the second patrol, switch it off if you don't want realistic availability dates.
-Open Basic.cfg and edit two lines:
.Under [Submarine1] change Month0=10 to Month0=9
.Under [Submarine2] change Month0=10 to Month0=9
-Install RUb or Beery's Flotilla mod, which corrects the dates (in addition to adding 1944 and 1945 start years).
Or, just start all new careers in October 1939.
Maybe Kpt Lehmann would like to fix this anomoly in the GW update patch?
EDIT: Actually, it is a problem created in part by the Grey Wolves mod. The stock SH3 dates have been left in Basic.cfg, but a 1939 start year has been added to Flotilla.cfg for at least the 2nd Flotilla. Thus, the two files have become out-of-sync.