Are there any buddhist terrorist or rebellion sects, or clashes between cultures or nationalities and others where buddhist identification is a major part of the cleavage between battling goups, as there are with hindu/muslim, christian/muslim, jew/muslim, catholic/protestant, etc. ?
The sectarian violence in Sri Lanka involves the 70% Buddhist majority, separatists and others in the Hindu minority (most notably the Tamil Tigers militants), and the smaller Muslim minority. Buddhist identification is explicitly invoked in the conflict by some members of the majority:
I believe this piece addresses that question directly.
There have also been violent attacks on democracy protestors by troops of the Buddhist/Hindu (difficult in that area of the world to extricate one from the other) kingdoms of Nepal and Bhutan in the early 90s. Very much Tiananmen Square-like on a smaller scale. In fact IIRC both incidents were in the repective Durban Sqaures of the capital cities.
Interesting, although it deals more with the hierarchy of an order with a state-religion establishment. He also seems to downplay the abuses since Chinese control a bit.
Burma is another state where anti-Christian and anti-Muslim violence and bias has been reported. However that should be taken in the context of a brutal junta that also seeks to control Buddhist institutions, even as it represses non-Buddhist minorities.
In Japan there is Aum Shinrkyo ( they of the subway gas attacks ) which is usually classified as Buddhist, though its eclectic theology allows for some dispute.