Yeah, the Log Book in the office has been a bother since v1.0.xx whatever it was for my original disk. All patrols are off by 1 in the numbering, and sunk ships are somehow dropped, often if they are a "repeat" of an earlier same-named ship. The numbering of the patrols is easier to understand, in that one fellow started counting the computer way with 0, 1, 2, etc., while the next fellow started counting like a human, unsing 1, 2, 3, etc... still not an excuse though for the discrepancy.
It sounds like you use Time Compression the same way as I do.
As for game file saving, it is best to do a completely new Save each time you do it, even if you make 15 saves on any given patrol. After you dock, you can then delete some of those, keeping one or two for the "just-in-case" situation you will invariably hit, such as a base transfer going awry...
- the practice does use up a bit of hard drive space, if that's what you're worried about. However, I would not think that re-using the name of an already deleted save would be a problem, but we have seen quite a bit of "strange" from the game... I usually do something like "P205074303" or similar, with the P being Patrol, 2 is 2nd patrol, 050743 is the date, and 03 is the save number of that patrol. You are allowed like 32 character names, so can be more descriptive than I am there.