There appears to be a bug on long running games or games that are saved and loaded over a day. I had a run that was 24 hours (saved and loaded the next day) and it was recognized only as 2 hours and caused some weirdness.
It's hard to say whether this is a Stats Companion or a *SCAN issue, but as *SCAN is only meant to read Stats Companion's outputs, I'm suspecting it's the former. At least, that's all I can assume without seeing the problem run file.