Why is cultural understanding often wrong?
I have a little difficulty understanding your question. are you asking why do we percieve slightly different behaviors as culturally different? I would say that for me cultural difference is a continuum or degree rather than difference. For example, as you wrote, prolonged eye contact is rude everywhere, but how much is acceptable might be different. Also for me the source of difference doesn't make it not culturally different. Every cultural difference comes from a source, socio-economic, geographic, historical etc. The different intellectual developments led to some cultural differences at least that's my opinion. Of course we can discuss if we should focus on differences or similarities among human groups. I would say should we choose between. I hope that was what you were asking.
P.C: to be honest, I was thinking about my own experiences and observations but when you think about one of the most popular theories about culture, Hofstede's four dementional theory, sees cultures in a continuem of four dementions (tolerence for uncertainty, individuality-collectivity, masculanity-feminaty, power of distance)(Hofstede, 1983).  It is not some cultures avoid uncertainty or seek it, but that some cultures/social groups avoid uncertainty or seek it more than other cultures/social groups for example. 
Hofstede, G. (1983). National cultures in four dimensions: A research-based theory of cultural differences among nations. International Studies of Management &amp; Organization, 13(1-2), 46-74.