I think Huntington is right in that the main conflicts of today are going to be culture based. I think he's wrong to be implying that its going to be CIV vs CIV, as if a civilization is a big monolithic bloc.

I mean, orthodox Georgians battle ortodox South Ossetians, arab muslims kill black muslims in Darfur (as well as christians), if there is civil war with Iraq it will be between Kurd, Sunni and Shiits muslims.

So long as people in poorer countries can see obvious differences between them, that can cause conflict. It doesnt matter if you are both muslims, or both orthodox christians, race and language can become the discriminant. I would say, we will see low intensity clashes of cultures.

The Bush administration's act notwithstanding :P

I don't think it is as simple as cultures not getting along. In all the examples you gave, economic and power advantages can be gained by one group triumphing over the others. These must too affect the motivation of these groups to go into conflict.

I'm unsure what you mean in reference to the Bush administration, but the USA's cultural colonization of the world too I think will mean culture is less of an issue as time passes.