[Silent Bob]

There's always a set cut off for any international flight, which is one hour. You're making the assumption that because you are there, at the airport (or in the vicinity of the terminals), you're ontime for your flight. But you were not at the counter 1 1/2 prior you were parking. The long term lot at JFK is just a bit outside the main airport terminals, and czech airline is in term 4, so given the distance and the time it takes just to park then get to the terminal, one can say yes you were definitely late for that flight. SO again the only issue you would have with czech would be the penalty that you might have overpaid.