Interestingly, if you run the barcode through a decoder app all it contains is your reservation number and (first?) date of travel. So either Amtrak has gone truly ticketless on their back-end system, or the ticket numbers are strictly used internally.

Out of curiosity, how much time passed between when you purchased the ticket and when it was scanned? My initial suspicion is that the conductor's hand-held scanner was out-of-sync with the live database and wasn't able to connect via a mobile (cell phone) data network. Of course, they should really have a formal procedure for this sort of circumstance...