Posting order is determined more by where did the conductor who collected your ticket turn it in at, than the order of your trip.
You mentioned the EB. I'm not sure which way you went, but let's pretend you went west from Chicago. First, you've already got a three day delay in processing, simply because even though the conductor lifted your ticket out of Chicago, it stayed on the train all the way to let's say Portland. If you're very next leg was to take the Coast Starlight south to LA, that ticket got turned in at LA.
Because of the volume of tickets that LA gets, they probably send daily shipments of tickets to the processing center. Portland on the other hand doesn't get that many tickets, so they may well hold their tickets for a few days, perhaps even till the end of the week, before they mail them to the processing center.
And Viola!, you have trips that post out of order. Granted it's a bit more compliacated than that, but you get the idea.
I see the same thing happen when I take Acela trips to Boston from NYP. I can go to Boston on Friday night, return on Sunday, and my return trip will invariably post first. It posts first because that ticket gets turned in at WAS, where they process things faster than Boston.