Amtrak has also been known to yield to reality by adding makeup time to the schedule at several points along a route. Often large amounts of it, resulting in the train either running early at the last few stations of a route and/or waiting at stations to leave on time if the delays are less than normal. The railroads basically want Amtrak to set schedules based on freight train speeds, running extra with plenty of time for sitting in sidings. And after all, Amtrak trains are short (fit any siding) and accelerate quicker than a freight train (so short deficits can be made up).

Not absolving the railroads over this, but it's easy to see why dispatchers would do it especially in PSR days with extra-long freights.