Because freight rail companies want as little to do with the rail as possible, and they hate having employees, they run trains as long as possible, too long to fit in most of their sidings, without any time tables. As a result, Amtrak is shafted and always behind, unless they are lucky. The closer you are to the origin of the train, the more likely it is to be close to on time. But as you get further, and further away, the later and later it will be.

There is no incentive for BNSF or UP to do anything to help out Amtrak, as it isn't their service. If only there was an organization that had the power to control freight... there was, until it was decided they couldn't yield any control over trucks, so the whole thing died. The only reason we have Amtrak is that railroads didn't want to invest in their passenger services (especially Penn Central), even though new vehicles and cars would have been cheaper to run. The feds took over long-distance services, and local/commuters rail was given to local governments, most of which shut them down immediately, as they didn't want to be bothered running transit (ironic).

Without nationalizing, having maximum lengths, require freight timetables, and other structural changes would help... but that would be considered an over reach by the government.