Does the status in SH3Cmdr say "In home base before patrol..." or "In other base before patrol..." before you load the game?
If the latter, then SH3Cmdr will assume that you have docked at a milk cow or other friendly port and will simulate same by changing the days in base value to 1 (plus damage repairs).
And as KLARCH says, always make sure you load the last "In base before mission" save from within SH3.
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