The sense of trauma continues and spirits of the dead are everywhere.
Driving through East Timor's western district of Bobonaro on the day Amnesty International released its report condemning East Timor's amnesties for war criminals, I experienced a compelling sense that the scars of 1999 and before had not healed. Perhaps a third of the houses I saw burnt in 1999 remain abandoned wrecks.
The people are rebuilding their lives, in many cases slowly, but the sense of trauma continues to manifest in sometimes imponderable acts, such as the violence of 2006.
Balibo, near the border, retains deep wounds from 1999 and from the 24 years preceding it. The house where the ''Balibo five'' Australian-based journalists were murdered is avoided by the local people as holding not just their spirits, but those of the very many others tortured and murdered there up until and during 1999. The Balibo House Trust, which works with the community, was recently told to shift the orientation of a proposed community hall to avoid covering the ground where there were still the spirits of murdered local people.
In the district capital of Maliana, a third or more of its buildings, including the house I occupied in 1999, remain charred shells. I noticed, as always, the Maliana police station where, in 1999, locals were told they would be safe from the rampaging militias. Instead, the police organised their bloody massacre. No one has been convicted of this crime against humanity, although its perpetrators remain well known.
East Timor is a country of rugged beauty, but it is impossible to look without knowing there has been great horror. Spectacular views from a cliff; bound people were thrown from it. Lovely beach; that was where the bodies dumped from the wharf used to wash up. Spirits of the dead are everywhere.
More than 100,000 people have been documented as having died directly as a result of Indonesia's 24-year occupation. The higher and more probably accurate end of this figure is about 200,000 - more than a quarter of the then population.
The popular feeling in East Timor is no longer so much for revenge, although that feeling continues to gnaw at some. More compelling is the desire for justice. For a people still coming to terms with the notion of the rule of law, amnesties for the worst offenders make a mockery of other legal claims.
East Timor's leaders have consistently played down pursuing war crimes and crimes against humanity, and have now passed a law to that effect. They have done so for two very pragmatic reasons.
The first is that Indonesia will never put its war criminals on trial, especially not over an issue that saw East Timor ''break away'' from Indonesia. The second is that pushing the issue will only anger Indonesia and powerful people within it. Regardless of how leaders might privately think, the costs are seen to outweigh the benefits.
Some politicians, such as President Jose Ramos-Horta, have also adopted a more formally Christian view in this overtly Catholic country of forgiving their former enemies. Indeed, the President has been widely criticised for his excessive leniency in granting amnesties, such as for war criminal Marternus Bere, who was caught in East Timor on an indictment for cold-blooded murders in 1999, but released last year under an executive order as a result of blunt diplomatic pressure from Indonesia.
Under East Timor's constitution, the President can grant amnesties, including to war criminals. However, even this controversial authority is of a lesser order to a blanket amnesty on war criminals.
There is an argument that a country and a people need to move on, to put the past behind them. Indeed, there is a common trait among the East Timorese that they have very long memories, that grievances can become inter-generational and that clan feuds can run beyond knowledge of the slight that caused them. There is no doubt this is unhelpful for a people trying to find their way in the 21st century.
But, more importantly, rule of law is not yet well embedded in East Timor, its police still make far too many ''mistakes'', its judiciary is often poorly trained, too few in number and disinclined to spend much time outside of Dili, in the villages where most people still live.
There is now a move to complement formal law with traditional law. This ''traditional'' law is often inconsistent, favours the powerful and is not so traditional. But it is available, works well enough and people have faith in it for that reason.
And then they look to the lawmakers in Dili and the amnesties for the worst sort of criminals - war criminals - and they wonder why they should acknowledge a system that is already struggling when their commonsense notion of justice is being flouted.
The price paid for being a small and still vulnerable country with big and pushy neighbours - certainly Indonesia, sometimes also Australia - is very high and it sticks in their throat.
Perhaps some compromises must be made by a small country simply to survive. But no one should be surprised if, sometimes, the anguished leaders of a traumatised people forced to make unpalatable decisions lash out, in Australia's case at those least likely to bite back.