I have run into a similar problem at LAX TSA couldnt scan my BP issued in HNL and I was instructed to get another one at the AA desk.
Unfortunately the AA first line was running very slowly and having taken an hour to process one pax the agent went on break leaving me with 15 mins to make the flight.
Eventually I managed to get a BP which was again rejected by TSA scanner- this time because it was actually someone elses BP that had been handed to me... back to the queue to be told it was now too late to be issued a BP, after much persuading I was issued with another BP which was rejected by TSA for being too late for the flight!