The trains don't seem to stop for very long, for about 1 second or so. Or am I not interpreting it correctly?

I don't think the 2d version is in realtime. I checked on google maps the journey from Shinjuku to Yotsuya on the red line is 11 min long, but on the 2d map the train does it in less than 10s. Plus, each time you reset the page, the positions of the trains are reset. Still it's cool way to see the activiy on the subway network.

It's working perfectly for me

The 3D version sure is cool but the 2D version would be much more usable.