Weather, heavy traffic, shortage of crews available to move trains, shortage of crew shuttle drivers, etc. Weather presents itself not just as snow or slick conditions (on rails as well as roadways traveled by shuttles and rail-related personnel) but also as extremely low temps, which not only impacts train handling (air flow) but can also force trains (freight and Amtrak) to run at reduced speed.
[weather.com]
One more thing that continues to be overlooked by most observers from outside the Northwest is the fact that coal and crude traffic has not dropped off here like it has elsewhere. At least one railroad in the region has chosen to limit loaded crude trains to daylight-only movement over mountain grades during periods of extremely low temperature. Trains have been getting parked in sidings and on sections of 2MT to the point where a hundred miles or more of main line is effectively reduced to single track, leaving no choice but to fleet crewed trains through in one direction at a time, Amtrak included. This time of year, it also becomes common for the Empire Builder in either direction to be pressed into snow coach service, stopping to pick up and/or drop off crews wherever there are freights tied down en route.