What happens if your ticket--always the old fashioned type printed out by staff at the station for me--isn't scanned? On a recent return trip from Gainesville, Florida to Washington, DC in a roomette I don't think it was ever scanned. Am I missing out on my points? Or something else could have happened while I was on board?
It depends on whether that "ticket" was a paper value ticket or an e-ticket boarding pass printed for you on ticket stock.
Either could be printed out by station staff on the same stock. An eticket boarding pass will have had a bar code on it, a value ticket would not. Your underlying ticket type determines what was actually printed out on that stock.
Situations requiring paper value tickets have gotten rare. Reportedly one of the last remaining value ticket holdouts, open sleeper tickets, are now e-ticketable. About the only situation left is when part of the reservation was on an interline/codeshare carrier, such as a bus company, whose systems are incompatible with Amtrak e-ticketing. In those cases, the entire reservation will drop to paper value tickets including Amtrak segments.
So, in order to answer your question, more information is needed than just "the agent printed it".
1. Did your reservation email include an e-ticket boarding pass PDF or did it contain instructions to pick up your ticket from an agent or kiosk before departure? Was the email titled "Reservation Confirmation" or "Reservation Confirmation and E-ticket"?
2. Was there a segment on another carrier, such as a bus or ferry, on the reservation?
If you had a value ticket, the conductor would have taken the ticket coupon and pouched it, leaving you the receipt stub of the ticket. He would not have scanned it as there would have been nothing scannable. If that is the case, you ought to receive AGR points for the trip once the ticket coupon is processed through Revenue Accounting.
If you had an e-ticket that wasn't scanned, it is possible the SCA simply told the conductor you were onboard and he checked you off, the equivalent of scanning. That is a practice I do not trust, having once been assured the conductor had me without having scanned my ticket when he hadn't. If that is the case, that he checked you in without scanning, your AGR credit should show up within a couple days. The other possibility is it wasn't scanned and the conductor didn't check you in. In that case, you would appear as having been a no show without getting any AGR credit for the trip.
The place to start is to know what kind of ticket you actually had, not just that you picked something up from an agent, which in itself is not indicative of anything. If you aren't not sure, look at your email, that should show what kind of ticket you had.
If you are sure you had an e-ticket and credit has not shown up, contact AGR and tell them you traveled but your ticket had not been scanned. They may be able to resurrect the points.