In order to find a comprehensive answer to this question, please start reading on p. 325 of Guns, Germs, and Steel. Diamond’s discussion of how these pockets of languages came to exist starts on that page and continues through the end of the chapter. As with many things in this book, Diamond’s answer to this question has to do with who got farming first.
Diamond argues that the three language families that now exist only in pockets were once spoken over broader, contiguous areas. In other words, these languages all had their own home territories where they were spoken. As the years went by, however, their speakers were overrun by people who spoke Sino-Tibetan languages. The reason for this is that it was the speakers of Sino-Tibetan who first developed agriculture. Because they developed agriculture before the speakers of the other languages, the Sino-Tibetans were also able to develop other things. They became civilized, developing technologies and more sophisticated and centralized governments than the other groups had. They developed writing and they came to carry the germs of infectious diseases. Because they had these advantages, they spread out across Southeast Asia. As they spread, the speakers of the other languages were pushed into marginal areas and those areas stopped being contiguous. They were isolated from one another in relatively small pockets.
Thus, these pockets of languages other than Sino-Tibetan languages came about because the Sino-Tibetans got agriculture first and thus became richer and more powerful than speakers of other languages. They then spread out across the region and forced the speakers of other languages into the marginalized areas where they now exist.