That's weird, I've always started in the 2 Flotilla with a Type VII and it puts me in Wilhelmshaven. That's in August 39 but it should be the same in September.
But your choice of flotilla will determine which base you start from - the flotillas are assigned to a particular base which depends on the date, in September 39 the 2nd is based at Wilhelmshaven. If you are in 2 Flotilla, you will start and end your patrol there; if you start from a different base, you're not in the 2 Flotilla.
When you select the 2 Flotilla in Commander to start a career, and then load the game and select that kaleun's names to start a new career there, and get to the screen where it shows the little map with the different bases marked up in the top right - there's a section to the left where you have to click on the forward or back arrows until it shows the flotilla that you selected in Commander. It won't default to it, you have to make sure you go through the list and select the same one.
If you have 'historical u-boat availability' checked in Commander then you can't start in Kiel (2 Flotilla) and get a VII, as 1 Flotilla out of Kiel only has Type IIs. If you are telling Commander to put you in 2 Flotilla but not also selecting that flotilla once you get into the game, I don't know what it does...
