If you got an upgrade on an eBay ticket, then that conductor did not follow the correct procedures and call into Amtrak to block out the room and get the price. Either that or the person on the other end of the phone wasn't paying attention to their job.

As for an AGR award, you can always upgrade those on-board, there is no restriction on those regarding performing an upgrade. On the other hand it can be kind of wasteful to do an on-board upgrade with an AGR ticket.

Normally when doing an on-board upgrade, the agent at the other end of the phone looks at what the low bucket price for the room is first. Then they look at the bucket price of your current ticket. If you paid anything above the low bucket, the difference between the seats low bucket price and what you paid is deducted from the price of the room. Since you paid nothing, you get no credit.

Now if you have a coach seat, that's probably not totally horrible, although one really should have simply saved your points for the day that you could just book the sleeper upfront. However, if one had booked a roomette award, upgrading to a Bedroom means that you get zero credit towards the purchase of the Bedroom.

In other words, you just threw your AGR award out the window. You spent all those points for a roomette and then got no credit towards buying a Bedroom so you paid the full low bucket price for that Bedroom.