Points for changed ticket?
 

I had to change a return somewhat last minute, resulting in a higher fare. I see that I only got AGR points that match the original fare. It's a Northeast Regional so not a huge amount of money / points, but this seems wrong.

ANybody know what the actual policy is?

It should be based on the actual ticket collected which would be the higher-priced train you changed to. I would call it in.

Yep - you should get the points based on the actual ticket collected.