The peace has held but the euphoria surrounding the MoU gradually diminished. It became clear that people's dreams for justice were not about to come true and that they would need to pursue their dreams a bit longer before enjoying their rights. When the Law on Governing Aceh(LoGA) came into effect on 1 August 2006, its many compromises on human rights issues cast a thick cloud over the peace accord.
The establishment of a human rights court and the truth and reconciliation mechanism were laid down in the LoGA with clear time limits (12 months), ostensibly recognising the difficulties Papua experienced establishing the human rights court availed by the 2001 law on special autonomy. Yet these deadlines have since passed. It appears that what were once primary human rights agendas have become perceived as bad ideas and there is unwillingness to make them happen.
The human rights court issue also suffers from multiple interpretations. Although GAM negotiator Nur Djuli announced early on that the Human Rights Court (HRC) would have retroactive powers, according to the LoGA (Article 228), the HRC can only try cases of abuses occurring after enactment of the LoGA, rendering it meaningless for resolving past human rights crimes. Looking back to the period before the signing of the MoU, various people involved in the process indicated that negotiations on human rights would be conducted with a spirit of 'looking to the future', and indeed the negotiations almost collapsed over the principle of retroactive prosecution. Central government's standpoint has not yet changed – or at least dares not change due to weak political power. Retroactive prosecution for human rights crimes is still technically possible, however, through Law No. 26/2000 on Human Rights Courts dating from the year 2000. This law allows for serious human rights violations prior to 2000 to be tried in ' ad hoc human rights courts' established by the president with the agreement of parliament. In theory Indonesia's National Commission on Human Rights (Komnas HAM) takes its findings to the parliament, which then decides whether there was a gross human rights violation and if so, can establish an ad hoc court.
For crimes after 2000 regular human rights courts may be used, such as the one established at Medan in North Sumatra province. However, as noted, although this court technically has jurisdiction over Aceh, and therefore fulfills the MoU stipulation that a human rights court be established for Aceh (no other court fitting this description has been created since the passing of the LoGA), no cases relating to Aceh have been heard there. The core obstruction to both the retroactive and more current prosecution of human rights violations is the same: the government and parliament in Jakarta do not give the necessary support for the judicial system to work. The law needs to be amended to eliminate parliament's political role in judicial practice, and to provide Komnas HAM with sharp enough teeth for it to offer a feasible domestic remedy to injustices. At a military ceremony attended by retired generals of TNI and POLRI in Jakarta on 28 April 2008, senior figures expressed their explicit rejection of investigations being conducted by Komnas HAM. This illustrated the narrowing political support for such investigations. The Minister of Defense Juwono Sudarsono has publicly discouraged retired generals from complying if summoned by Komnas HAM, while President Yudhoyono himself keeps silent. The Minister of Law and Human Rights, Andi Mattalatta, accompanying Yudhoyono in receiving President Marti Ahtisaari in Jakarta on 7 May 2008 to discuss progress on the peace process, explained to the press that because government had given amnesty to GAM, it would not be proper to enforce the law against the TNI. The space for fair and just remedies for Aceh seems to be shrinking.