Unfortunately, several of the Class I freight railroads have been preventing Amtrak from running on time recently.
BNSF has had total system meltdown on the Empire Builder route. It's messing up their freight trains something awful too, so maybe they're doing their best. The Southwest Chief route they usually do a lot better on; you had terrible luck coming back from LA.
NS is also having a system meltdown from Chicago to Cleveland recently, unfortunately; they're usually pretty good.
CSX (who control Albany-Cleveland on the Lake Shore Limited route) is particularly bad everywhere and at all times and just doesn't seem to care.
I suggest, in future, before considering Amtrak, check out the route you're considering on
http://www.amtrakdelays.onlineschedulingsoftware.com/ . Some routes are pretty good about running on time; others, unfortunately including most of the cross-country ones, are not.
I hope you'd consider taking the Pacific Surfliner from LA to San Diego or the NE Regional from Boston to NY to Washington, which are much more reliable trains. They run on track controlled by PASSENGER train operators, so they don't have the same problems as trains running on track controlled by Class I freight railroads.