Unlike Kosovo where communists were involved, Indonesia is a country run by a military that is supported by the western powers and led by the United States. This seems to be a stumbling block when it comes to human rights and other issues of political passion, with money being more important.
In Kosovo it was also a chance to convince Europe that they still needed US troops everywhere to defend them from the evils of "ex-communists".
In East Timor we already are in control, and we don't want to blow the nice deal we have going there...

Reports say that 150,000 people have joined the 250,000 who have been in hiding in th mountains for 14 years. The Indonesian military supported militias are shooting and burning everything in site, including the churches. The military is doing nothing!
We are doing nothing except asking them to provide security or the United Nations will do it for them.
Guess which one they will pick?

The Indonesians have already started to evict the journalists that they haven't been able to shoot. Soon enough everything will be under control and we won't hear a word about it for another 14 years...

Is it just?
Damn, this world sucks!

East Timor: Questions and Answers
East Timor Action Network
Z Mag Links on East Timor
Chomsky on Timor