As far as I can remember I didnt make any mods to the sub before the first tour. I'd read the bug report and was aware of it.
As for your first question, I dont remember seeing an "in port after patrol" save only the "in port before patrol" which according to the date/time stamp was before patrol 1 (the first time). And yes I did exactly what you thought I did. The latest save was the latest chronological save (cant remember what it said though - sorry, I'll try to give more info in future
).