When you purchase two separate tickets you run this risk. It's not US Airways fault that your inbound flight was late and because you purchased your ticket separately they are only going to treat you the same way as any other person who arrived late to check in. Once the 30 minute check-in window closes the agent's computer won't allow a late check-in. I know this because I was checking in next to someone in Phoenix who arrived late for a flight. Only a supervisor can override the lockout and apparently the supervisor at JFK was unwilling to do this. Probably because they knew that less than 30 minutes is not enough time to clear security and be at the gate for the 15 minute cutoff time there. They did not want you to have the expectation that because the rules were bent for you at the check in counter that they wold then allow you to board the plane if you missed the boarding cutoff as well.
As for your ticket having no value, that statement was incorrect if it was indeed 30 minutes before departure. Your ticket, per the fare rules, has value as long as the scheduled departure time hasn't passed. Technically, they don't void the tickets until midnight. If you were, in fact, at the ticket counter with 30-31 minutes to spare this shouldn't have been an issue.
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