I have an untested theory that your reputation affects whether a station will attack you for having a fine (not a bounty).
I played for weeks in federation space, went to stations to pay off fines all the time, never made any special effort to avoid being scanned, and was never killed by a station. I was Allied with the Feds.
Then I moved to Empire space where I was neutral, picked up an accidental fine, flew to a station, and got blown up.
I find it highly unlikely that I avoided being scanned every time back when I was in Fed space - I must have paid off fines 20-30 times and never made any effort to avoid the scans, it seems that perhaps it's more than a coincidence that the first time I was killed by a station for having a fine was after a move to a neutral station.