Well I'm not "JP" by any means and haven't been living in Japan long at all, but I've yet to hear *anything* about this. Not that I'm doubting its truthfulness, just...haven't heard about it. And I take lots and lots of trains.
In what area is it? >.>
I saw ONE in Tokyo and asked my hosts (US Air Force) what it was. There were little markers on the ground that said in plain English "Ladies ONLY" and it looked all pretty and stuff. It listed really late-night hours iirc.