I am sorry you had to go through all that and i also had a bitter experience once and since then i always make it a point i do a ON LINE check in at least 30 Hrs before the scheduled flight.
It is really Unafair practice and no matter what is their justification this practice of taking money and selling more tickets that you have is not FAIR PRACTICE.
The justification they have is they want thier all tickets sold, but that does not give them the right to deney a seat to a person who has booked in advance. I wish the concerned airlines look at this and not show the passinger a sheet behind the ticket that has writings thatcannot be read even with a MAGNIFYING glass.