I had a similar experience with NWA in IND got into LONG check-in line later than I should have and asked an agent who was wandering around looking for passengers to pull up in line on flights later than mine. I asked if it was possible to move up in the line for my flight, was told no, too late.

I called a friend who was already checked in and waiting for the flight; he told me flight was delayed 45 minutes. Checked with the agent again with my newfound info, still no dice. Waited through the line and explained to the desk agent that I was late for the original time, but I understood that the flight was delayed. Agent checked and confirmed the delay and checked me in for the flight.

Not sure what would have happened if I had not had the inside info...

Moral of the story - I don't think Frontier is unique in mishandling this type of situation...