Interesting. I looked for some statistics and found that my experience of trains always late matches the rush hours (and I was always taking the train during the rush hours). More than 1 time every 2 days statistically the train was late in 2018 in Tokyo, during the rush hours. Based on the numbers from: https://toyokeizai.net/articles/-/330619?page=2 Based on the data here: https://www.mlit.go.jp/report/press/content/001328948.pdf I see a lot of suicides, which matches also my experience (I often read "passenger accident").

I guess you didn't take the train between 08:00 and 09:00. At 08:55 at Shinagawa with the sound of people walking at the same pace during the rush hour, the first time, I got dizzy and had to slow down.

But indeed after work I don't remember having heard the train was late. Maybe you worked at 10:00?