[Nyororin]

I really find all the stare talk fascinating as apparently I live in another Japan where this doesn`t happen. No one around is "startled" by foreigners, let alone giving them glares. Or maybe this is just me? Which leads me to wonder what other people are doing that earns them so much staring - especially as Japanese people don`t tend to give nasty looks in the first place.

I also had old ladies giving me dirty looks for sitting next to them on the subway.

Wait, next to old ladies? Were you sitting in the elderly/priority seating area? Because that should earn a glare regardless of where you`re from.

but when a foreigner complain like "I got a dirty look from a person who sit next to me" or "Nobody wanted to sit next to me", most of the times, they are breaking some rule.

I think this is pretty much accurate. I`ve been riding the trains for over 10 years, and have never had stares or people not sitting by me. I`ve never heard anyone talking negatively about foreigners/me.
I have however seen other foreigners sit down and take up two or three spots with their way of sitting, or plop their bag on the seat next to them when it is crowded in the train, or sit in the priority area without noticing, or keep talking loudly with friends, or be generally inconsiderate.
I have had other people with me who only speak poor or elementary Japanese THINK that other people were talking about them - when the other people were really talking about something completely unrelated. (And the lower level Japanese speaker think they were quite sly for "understanding" the people talking about them, saying something to the people who were talking - earning them stares and avoidance... Which is pretty understandable as I think I`d do the same if I were talking to a friend and someone came up and said "I understand what you`re saying!" or "I know you`re talking about me!")

Having seen far more people misinterpret normal things as being negative toward them than actually have negative things happen to them... I tend to take these accounts with a grain of salt. There is WAY too much "this happened to me because I was a foreigner!" and way too little "this happened to me because I was doing something something" - when most of the time it is something that would earn a Japanese person just as many stares. People aren`t going to not look when you do something that they find weird just because you`re not Japanese.

Seriously though, I have been waiting 12 years to catch someone saying something about me thinking I couldn`t understand them so that I could make some snarky comment - and have yet to find even one.