Do you live in Hokkaido? Or maybe on a really local branch? I live in Tokyo, take around four trains a day on many different lines and that is just not the case here.
My experience with Tokyo (I only visit about once a year, live in Kyushu) is the trains there are always off-schedule due to "accidents" :/
Sendai, Miyagi it is. Trains come in from a bit more country side.
I'd like to think of Tokyo As the exception to Japan. Having said that, all the pointing and calling is happenening everywhere.
In Japan they might be a little delayed. In Boston the trains just don't come at all. One time I was stuck on a train for four hours because a switch was frozen (normally a 40 minute trip).