We grab the system time and don't modify it when putting it into the FITs header as DATE-LOC. For the DATE-OBS we convert to UTC.
The windows Created Time should be the same as the time displayed for DATE-LOC.
I don't get what you mean about the system clock and the FITs header not matching. Are you watching the images as they come down and comparing that with the clock?
Thanks,
Jared