Also in that screen that comes up in the game menu when you load a career - the one that shows the choices for starting time and flotilla?
Above the places where you can choose different times and flotillas/bases, you'll see text (inserted by Commander) that will show you what time and flotilla you pre-selected in Commander. Just make sure that what you select matches it and you shouldn't go wrong.
Commander can't force the game to give you the starting date and flotilla you pre-selected in Commander, you still have to select those things in the game itself in order for the game to comply. But by telling Commander ahead of time what your choices are going to be, you let Commander know which of its date/flotilla-dependent options to deploy when it launches the game for you.
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