Five years later, after a very long inquest and a very long trial that saw David Eastman convicted, the presiding judge commented it had been the most extensive, intensive and expensive investigation in Australian police history. It had stretched locally, nationally and even internationally, with millions of pages of files, statements and transcripts.

The judge expressed no doubt in his sentencing remarks about that inquiry's professionalism, the verdict's safety and the evidence's cogency, particularly the forensic evidence.

Eastman, still protesting his innocence, was sentenced to life in jail, and was not released from prison until four years ago. That was after an inquiry, by retired Northern Territory and South Australian judge Brian Martin, found that the original trial had miscarried, and that much of the forensic evidence, particularly that associated with an "expert" from a Victorian police forensic science unit, was entirely unreliable.

Martin recommended the conviction be quashed, and thought there was little point in a new trial after such a passage of time. While Eastman was "probably guilty", he said, unnecessarily and gratuitously, there remained a "nagging doubt".

The ACT Director of Public Prosecutions, Jon White, thought Eastman would probably be convicted again even if the evidence in dispute were omitted. He challenged the Martin recommendations, and, ultimately, the ACT Supreme Court allowed a retrial. White said a prosecution could be started in a very short time, but most of the extensive delays before the trial started in the middle of this year occurred because the prosecution failed to meet court time tables about the production of its evidence.

On Thursday, a long-suffering ACT jury decided, after extensive debate during which some jurors changed their minds, that the evidence they had been shown did not satisfy them beyond a reasonable doubt that Eastman was guilty. Depending on the individual juror, that could mean anything from a belief that Eastman was completely innocent, perhaps because the defence had proven the alternative hypothesis, to a feeling that the "nagging doubt" was a reasonable doubt. Under the common law, it is for the prosecution to prove a person guilty; if they fail to do it, even a person probably guilty should go free.

It is plain from the comments by police, prosecutors and surviving members of the Winchester family that they continue to believe in Eastman's guilt, and reject the idea of now searching for the real killer. This is the problem in which outsiders, including the broader public, should be keenly interested.

Control over the investigation into the Winchester murder lay in the immediate underlings of Colin Winchester – people who were his friends and mates. They were emotionally affected by the murder, as well they might have been. They were protective about his wife, and some of the first arrivals on the scene thought, almost certainly wrongly, her to be the obvious suspect, if not the only one. A cop who was there told me that one of the reasons why the crime scene was trampled over in the most amateur, incompetent but comprehensive way, was that there might be a need for some freedom of manoeuvre if the evidence pointed to Gwen, or perhaps to a disgruntled cop. It quickly became clear that Gwen was not involved, but by then the path to a bad investigation had been set.

Gwen was, of course, one of the police family. She and other relatives remained close friends of the investigators, and were loyal to the settled AFP hypothesis, even when other police, not in this particular tribe, expressed doubts about its sufficiency, or the lack of breadth of inquiries.

Her faith and devotion to the cause became a two-way street, used by the investigating team sometimes to suggest that to express doubt about the Eastman brief was to show disloyalty to her, or other relatives, or to reinforce a quite false hint that the team had undisclosed (but inadmissible) evidence against Eastman that conclusively proved his guilt and justified the investigation's one-track mind. Perhaps she needed to believe that, because otherwise it meant that the murderer was still abroad and that the crime against her husband, her family, the AFP and the nation was still unavenged.

Over a prolonged and undisciplined inquest, a farce of a first trial, and a much more sober and professional second one, there were changing judicial views of the admissibility of particular evidence. But there was never any supressed or secret evidence "confirming" Eastman's guilt. There is evidence, not fully disclosed to the jury, suggestive of the guilt of others, but nothing that has not come out over the past 30 years against Eastman.

What you saw was what you got.

Simply, the crime should have been investigated by a more detached squad, without any emotional overlay. And it should have been investigated by people of a more professional and competent mien than by local detectives who had learned most of their craft either from solving crimes in the fairly placid ACT, or with the help of a NSW police force we now know not only to have been deeply corrupt but also as complacent and tribal as the AFP.

Even when police were inclined to be fair-minded, and that was not always, the investigation became infected by AFP politics, and by tunnel vision, or, as some call it, confirmation bias. Under this, police see evidence that agrees with their present theory and ignore or discount anything that doesn't. There was nothing wrong with having a long hard look at Eastman. But the "hunch" among senior detectives that he was the one came long before there was clear evidence inviting questions about him. Other avenues of inquiry had been blocked because investigators in Team A had convinced themselves they had found their man.

The investigation was also compromised by a deep contempt entertained by former ACT police officers for people in the AFP whose careers had started as Commonwealth policemen. To the ACT people (who included Winchester, even if he had worked on national issues as well), many of the nationally focused people were not real cops, had little "street experience", had failed to acquire the cynical wisdom of the beat cop, "had never faced an angry man", and were fit only for guarding Commonwealth buildings.

Many in the other side thought of many of the former ACT police as hicks, with systemic corruption problems (if not ones that yet deeply compromised the whole operation) and with a serious problem of what one would call these days a "culture", particularly of misplaced loyalty to each other. Not a few journalists thrived on the mutual back-biting involved.

The "alternative hypothesis" was being investigated by the AFP's national units. The search for a killer at a domestic level – the one that came to single-mindedly focus on Eastman – was run by former ACT officers with a predisposition to doubt the abilities of national investigators and their conclusions.

The national team found a considerable body of evidence "pointing" to Calabrian involvement, including a marked upsurge in (intercepted but almost indecipherable) communications in the immediate lead-up to the killings, strange and obviously contrived alibis, if sometimes very proximate to the murder scene, and reports from informants pointing to travel into Australia and quick exits by Italian 'Ndrangheta operatives. There was a lot of noise, but, so far, nothing positive pointing to anyone in particular.

When reports of this team – recommending further follow-ups – were put in the hands of the major investigation, the collateral investigation was closed down as not having produced anything worth follow-up. By then, the ACT group was convinced they had found their man, and anything else was a waste of time. From now on, any further investigation into the "alternative hypothesis" tended to be with a view to discrediting any fresh evidence pointing in that direction, or ignoring it – in some cases, not even bothering to investigate suspicious alibis.

The case also involved, as was suggested from the start, clear police misconduct, if rationalised at the time as dodgy but reasonable. Eastman had been mentally ill, and was plainly still affected by symptoms, including a hair-trigger temper and a tendency to make threats (if ones rarely carried out). Police engaged a psychiatrist to advise on how to deal with him. Some of the investigators believed, perhaps because of that advice, that Eastman might "crack" and say or do something that absolutely and unequivocally showed him to be guilty. Not to put to fine a point on it, they baited him, carried out in-your-face intrusive surveillance so that he was never alone in the streets. Investigators, whether in their own time or as a part of the investigation, would ring Eastman late at night, harassing and abusing him. Though the campaign was obvious to everyone following the case, including prosecutors and judges, and was extensively reported in The Canberra Times, bland police denials of wrongdoing meant no action was taken. In a different environment, police misconduct would have fundamentally compromised the prosecution case.

Eastman got lucky, thanks to a communications specialist, and was able to prove that some of the harassing calls came from investigators at the police station. This forced an internal investigation by officers uninvolved in the murder inquiry but, as evidence at the Martin inquiry established, the guilty parties, and some of those leading the investigation, lied to their brother officers. One of those shown to be involved later became the commissioner of another police force.

Eastman was his own worst enemy, with a capacity to alienate, or round on, even strong supporters. But the criminal justice system is often pitted against the unpopular, the unlikeable, the mentally ill and people from minority groups, including Aborigines, recent refugees and the homeless. The true test of a police force and justice system of integrity is whether such people can get a fair shake and a fair trial, not whether some articulate and well-heeled member of the middle class can.

Was it Eastman? Possibly. Are we sure? No, we cannot be, because of inadequacies in the investigation. Inadequacies of AFP leadership, from the top down to operational areas, inadequacies in skills, professionalism and detachment. I do not believe for a second that police set out to "fit him up", but I do believe that a better and more fair-minded investigation would have looked wider, looked longer and withheld judgment, as well as punishment before sentence.

This case has cost the taxpayer more than $30 million. It was high profile from the start, with those involved knowing their every action would be under scrutiny. If they behaved so amateurishly and unprofessionally with such a case, with what confidence can citizens, or jurors, or magistrates have in an ordinary common or garden case?

It will be claimed, no doubt, that it is now ancient history, with all of the investigators now retired and the AFP much changed, not least with its new technical capacities and focus on terrorism, drug importation and paedophilia. Likewise with deficiencies in the prosecution, including the failure to look behind forensic witnesses found by the Martin inquiry to be more or less making up their findings. What possible purpose could be served by a further inquiry into what happened?

Yet it is plain that the AFP and the ACT DPP have never faced up to the fundamental flaws and problems of the way they assembled their case, and that the modern successors of those who let us down from 30 years ago are still in denial. It seems that one of the reasons the DPP was so determined to continue a prosecution to the bitter end, even after Eastman had served nearly 20 long and hard years in jail, was to appease a police force not used to criticism, and a family that likewise could believe no wrong of the investigation.

The AFP was formed by, and over the intervening period has been led by, people who learnt their skills at the knees of officers not up to the task. The AFP hierarchy remains complacent and unwilling to look for lessons. It is from such mindsets that we have had the Muhamed Haneef cases – again showing systematic failure including confirmation bias, from top levels down. It is from such a force, so resistant to any sort of examination of conscience, that we must rely on in significant cases of terrorism, where investigations are necessarily somewhat unaccountable.

The AFP is the only Australian police force that has not been subject to a properly independent external inquiry over the past 30 years. The Winchester debacle could be a good occasion to have one. What is missing is the political will, either at the ACT or the national level. Politicians and bureaucrats are more afraid of the AFP than it is of them. It's about time the situation was reversed, if only because of the very poor quality of the service provided.

Jack Waterford has been involved in the Eastman case from the night of the murder, and was involved, from 1994, in arguing that the case against Eastman was flawed and that his guilt had not been established.