The ticket lift is seen more or less instantly, and every conductor's iPhone would see that your ticket had been lifted by another conductor. However, processing for revenue purposes and other things are still done in a batch mode. And that includes processing each day's scans for AGR as a batch on Amtrak's mainframe, which is then transmitted to AGR's system.

And therefore it would seem that something somehow held up the processing of the batches from that weekend. What that is, I have no idea. But I was out traveling that weekend too and I know that my tickets were lifted properly; so it's really a matter of waiting for Amtrak to figure out why those batches weren't processed.