The Indonesians absolutely brutalized these people, as well as many of the other unique populations within their boundaries. A Marine friend of mine was sent into East Timor during '99 as a "peacekeeper" on the U.N. mandate, I believe. He told of the Indonesian army appropriating all of the local fire tankers, loading the tanks with gasoline and driving around the cities dousing and lighting anything and everything. Bodies were everywhere, and the citizens domestic hogs would gorge on them by the roadside. The people of course wouldn't touch the pigs after that.
I would expect that the Timorese must be suffering from mass PTSD, a wrecked economy and the Indonesians still taking a shit on them whenever they can.
Australia is doing what they can to assist, but this only further drives a wedge between them and the Indonesians, who prefer to spend their time suppressing the press and free speech, subjugating populations that don't embrace the corrupt government by forced relocation and warfare, commuting prison sentences for religious zealots who advocate bombing bars full of Australians, executing or jailing for life Australians who are found guilty of drug smuggling in courts that have never found a single defendant innocent, and other shit like this. My point here being, Indonesia sucks. While East Timor now has it's freedom, they've got nothing with which to get their feet on the ground, but plenty of machetes.