Is it true that Japanese don't want to sit beside us on the train?

Many gaijin claim that Japanese don't want to sit beside them on the train, and that therefore they often choose another sit even if there is plenty of free sits around the gaijin, or that they could move to another sit or even stand, rather than keep sitting beside him. Well, is there any foundation to this view or is this just a kind of paranoia?
I've been in Japan for 12 years, and this means that I took the train in Tokyo about 5,000 times. It happened to me a few times that my neighbour moved to another sit. The first issue is: if this happnes once every tousand times, is it enough to define a racist attitude against foreign passengers?
Even if this would be the case, I also have to admit that "I" did move to another sit much more often than my japanese neighbours did.
Why? Well, in some cases just because I didn't notice that my neighbour was a homeless. I don't have anything against them, they are good guys, but, since they don't have many chances to take the shower, it's also natural that the smell emanating from their body could be something that we "civilized" shower takers are not used to.
Of course, if this was the only reason for me to change the sit, the situation could seem even worse. It could mean that japanese avoid sitting beside us because they think we smell!
But this is not the case. Actually, the fact of my neighbour being a homeless is just one of the reason for my changing sit, but there are some other reasons. Another sit can appear more "tempting", for following reasons:
1) Another available sit is the last sit (or the first) sit of the row, so that you can lean your body on the sit's arm, and it's confortable if you have to sleep.
2) Another available sit in a row of 2 o 3 free spaces, so that if you sit there you have more space tu stretch your body.
3) Another available sit is close to the exit, thus being convenient if you are on a hurry.
4) Another available sit is between thin people that don't read the newspaper.
If you are already sitting, there must be quite a big motivation to induce you to change a sit. Former motivations could be enough, expecially if you are tired and you really need to lean (see 1). Also, most of the foreigners are fatter than the Japanese, so that 4 can sometimes be a motivation to move from a sit beside a foreigner to a sit between Japanese. But, if you are standing and there are many sits available, how do you choose your sit?
Choosing a sit on a train between the available ones, can seem a simple action, but there are actually many thoughts involved.
I did following considerations:
1) Boys usually prefer to sit near girls than near other boys (I don't know if the opposite it's true for girls)
2) As a neighbour, people usually prefer a thin person than a fat person
3) People who are not reading, not listening to music, not eating are preferred
4) People that are alone are preferred to people who are with friends
5) People who look "normal" are preferred
6) People that look "good" are preferred
7) And yes, Japanese are preferred to foreigners (but I guess this is true not only for Japanese, but even if to choose is a foreigner!)
I think that everybody would agree to (1)-(6), but (7) could be surprising. The fact is that actually, Japanese have a good reputation even between foreigners (beside being usually thin) and, even if many foreigners would deny it, I guess that in the instant when one has to choose, it's probable that in most cases even a foreigner would choose a japanese as a neighbour.
Most people are not conscious about how they choose a sit, but I believe that almost everybody does a sort of calculation. It may be something that has to do with survival instinct. In some cases it can happen that a Japanese, even if he likes foreign people with his rational self, could choose to sit beside another japanese instead than beside a foreigner, just because he feels safer there.
Well, it's something very instinctive and I don't think that this should be judged or condemned, also because it can happen to anybody.
The point is that, people who live in foreign countries usually have a kind of complex, that makes them feel themselves subject to racism even if they are not, and makes them interpret as racism other people attitudes that are just normal.
So, for example, if a Japanese is sitting on a train in Japan and he sees me choosing another sit instead of sitting beside him, he would not think that I'm avoding him: he would probably just not think anything. But if the same thing happens when this person is in foreign country, in Europe for example, then he could think that I am avoiding him on purpose, because the complex works in this way.
Basically the way one choose a sit on a trains means nothing about this person's mentality. I guess that we should just stop judging it and stop worrying about it.