You are saying that the system crashed in the morning for about an hour, but this lady was denied checking her baggage in the afternoon. That still doesn't explain anything.
It's a ripple effect. Once the system came back online, it then became the responsibility of a down-line station to ticket everyone who had boarded while the system was down. Passengers on a train need tickets, especially if they plan on connecting somewhere or going on a round trip. Amtrak's baggage system is excellent at moving luggage without losing or delaying it, but it is a little archaic in the time it takes to get bags ready to load. From my experience, it's not too hard to get a bag to a station located on the same route as yours; they'll have preprinted tags for that. If you're connecting, however, that's when things take a little while to prepare. They have to fill out tags by hand with train numbers, destinations, and locations of transfer for each bag checked. It should be modernized, yes, but this is the system they have to work with at this time.
The timing of the event in this thread matches well with my experience on that day, so that's why I theorized that the checked baggage issue was related to the system crash. People in Columbus, WI, were denied checked baggage for a train that called at 2:00 ET even though the system was back up before then just because there were so many tickets to print out and only one person to take care of it. It wasn't that big of a deal on my train because there's a lot of room for unchecked baggage on a Superliner-equipped train, the track is at ground level, and it's only three stops and 150 miles to Chicago where there's a lot more help available to deal with baggage.
I guesstimated that ARROW was out for an hour; it easily could have been longer. I can narrow the outage down to a specific range of times (and even though the events occurred in Central Time, I'm going to report them in Eastern Time to help compare): Whenever I'm scheduled to be on a train, I always check its status in the morning just to see how it's doing. At about 10:00 AM ET, I checked the website and saw that my train was running on time. At Noon ET I wanted an update and I got a system error through the website. Figuring that something was up with the web site, I called Julie, who was also unable to do anything. When I got to the station at 1:30 PM ET, I learned that the computers systemwide had been down but were running again. I didn't ask how long they were down; it wasn't my business. None of the passengers who boarded at La Crosse (scheduled for 11:47 AM ET, the train was a few minutes down) were able to retrieve tickets if they didn't have them in hand when they got to the station, and my station agent was frantically trying to get those tickets together in the half-hour he had available before the train arrived. Once aboard the train, passengers without tickets were to go to the dining car to collect tickets for the other legs from the conductor.
So, sometime between 10:00 AM and 1:30 PM EDT the system was down. It is entirely plausible that the system outage affected passenger boardings at both Meridian and Tuscaloosa. If you were to add those two stations together with the people in Birmingham that needed tickets, that's a lot of printing and it's easy to get overwhelmed. (This is what happens now that Amtrak charges a fairly hefty fee to have your tickets mailed to you; a lot of people aren't going to show up at the station with tickets in hand.) I could see the agent having time to deal with some but not all of the bags. Because of that, I could understand not collecting any of the bags instead of creating a rift between passengers who got special treatment and those who did not.
My question for those of you familiar with the Birmingham station is this: how do the handicapped get to the platform? There has to be some kind of publicly accessible elevator, I'd think, and the true issue is why weren't more people directed to that ahead of the train's arrival so that they could use it to ferry their luggage upward. That, and again, why no one stopped to help anyone else.
Look at it this way: A low-bucket one-way coach seat from Birmingham is $31 to Atlanta, $35 to New Orleans. That voucher can get you a long way towards a couple of cool places.