So, getting back to the OP's situation. Is this one case where calling someone is advised? I assume that the phone charge is waived with certs. Do the agents have the ability to hold N seats at the fare (assuming they were available at the start of the transaction) and run each through on a different PNR?

It is more than likely that the OP only had 2 seats in the fare bucket, but there could be a situation where there were three and then somehow IM (or some other customer) takes the last one before the third transaction went through.

I assume using book and hold on .com wouldn't have helped in this case.