You must remember that the days in base value means just that - the number of days that you will spend in the command room between the end of your last patrol and the start of your next patrol. So, let's say you finished your last patrol on 1 July 1940 and the randomised days in base value is 20. When you dock and reenter the command room it will still be 1 July 1940. You buy a few things, paint an emblem or two and the date increases to 15 July 1940. Still irrelevant. However, when you start your next patrol, you'll find that the start date is 21 July 1940. Of course, if you do a few major upgrades and the in base date goes beyond 21 July 1940, your patrol will start on the later date.
If this is not the case, then you may have some problems with your installation of SH3 Commander. Try setting a fixed period as Bladeheart suggests and post back if the last patrol end date + the days in base value does not equal the day that you get back into the sub for the start of the next patrol.
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