Two additional reasons for delays:
1. New priorities (shorter end-to-end times) for BNSF Z trains with UPS traffic. I believe that if BNSF fails to deliver a Z train on time, the customers don't have to pay - or something like that - and that probably adds up to a lot more $$ than FRA fines.
2. Bakken Shale oil extraction activity west of Minot. Much of this oil will be shipped by unit trains, and the loop tracks to load oil are under construction now. At the moment delays are occurring because shipments of pipe and fracking sand are set out on sidings for transloading, thus preventing meets on these sidings. In the future there will be unit oil trains adding to congestion on the line.
I still give BNSF credit for good dispatching, or at least that was the case on my two recent trips (#7-29 and #8-6). While some trains are delayed up to two hours for freight issues, the really late trains (>4 hours) have encountered something more major. And if Amtrak wants the freight RRs to take them seriously about needing to stay on schedule, they ought to do a better job of getting trains out of Chicago on time.
Mark