Wow this is fascinating. Clockwork, like everything else in Japan. I first noticed this when in Kyoto. The driver would point at the schedule, speedometer, sensors and all else. I found it slightly odd but made a mental note to google it later, which I eventually forgot.
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.
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).
