Uuummm...IIRC, starting in August of '39 on any date other than the 1st of August, thoroughly "confuses" the game and you will not get the 5-day shakedown patrol mission.
I'm sort-of-sure, but not absolutely positive, that if you start any time after the first (and certainly after the 6th, when you would have completed a 5-day patrol that started on the first) GWX "assumes" you did complete the shakedown patrol and assigns a follow-on patrol instead (usually follows the "waiting positions" boats were sent to in mid/late August)...or is my memory totally FUBAR on that? Could be...
I'm also just curious about which option for days in-port between patrols you have selected in SH3 Commander, random or specified? Maybe that influenced the start date of your "second" patrol.