UP's freight business increased substantially in a short period of time and they were caught with their pants down. They don't have enough train crews to move all of the trains that they need to run.
So in addition to track capacity issues, which are severe, things are made worse by the lack of crews. They can't get trains into the yards fast enough, they can't get them out fast enough. This causes train crews on the mainline to go dead on time, meaning that they've exceeded the Federal maximum work hours.
So now you've got a train parked on the main line that can't move. Since they don't have enough crews to go around, it can sometimes take a few hours before a new crew can be found to move that train into a nearby yard or towards its ultimate destination. And things just snowball from there, with other train crews including Amtrak, now exceeding their maximum hours, since they were delayed by the first train that stopped.
As for the schedule change, the only one that I'm aware of is a one day a week termination at New Orleans due to track work east of New Orleans.