The final results of the south Sudanese independence referendum were officially announced on Monday at 11am in Khatoum. The outcome was not a surprise. Almost 99% of southern Sudanese voted for secession. Africa’s biggest nation is going to be split in two.

In a sign of harmony the final figures were formally presented to Sudanese president Omar al Bashir and southern president Salva Kiir at the presidential palace in Khatoum. It was an extraordinary conclusion to a process that many feared could spark a return to civil war. In the end the ballot was remarkable for its overall lack of violence.

Regrettably there are signs that the process of separating north and south will not be so smooth. In the past few days at least 50 soldiers have been killed in what appears to be an outbreak of mutiny in the Sudanese army.

Initial fighting broke out on Thursday and Friday in the Upper Nile State capital of Malakal. This fighting was believed to have been sparked when former pro-Khatoum militiamen were asked to surrender heavy weaponry and tanks. The ex-militiamen are deployed alongside regular northern troops, but their roots are in the south. As the northern army prepares for withdrawal the former militiamen — and possibly others — are proving reluctant to leave.

Twenty people were killed in the initial mutiny, including two young children and a UN driver caught in the crossfire. Since then outbreaks of infighting have spread to other areas of the oil rich Upper Nile State. In two separate clashes on Sunday at least 30 soldiers were killed. Intense fighting reportedly included the use of mortars and heavy artillery. Further battles have been reported in at least one other remote location, but concrete information is so far unavailable.

As the south prepares to deal with the challenges faced by its new-found freedom, Sudan’s north continues to be buffeted by the winds of change raging across the Arab world.

Public demonstrations — albeit on a relatively modest scale — have been seen throughout Northern Sudan in recent weeks. Initially these protests focused on rising prices for fuel, food and sugar, but as the scale of popular uprisings in Tunisia and Egypt has widened so has the scope of Sudanese demands.

Reaction of authorities to protests has so far been predicably brutal. Police beatings of protesters have been routine, large numbers have been arrested. At least one student has been killed.

The climate of dissent in Northern Sudan has also resulted in a suppression of press freedoms. At least four newspapers have been censored over their coverage of the protests — two have been shut down completely. Several journalists and staff are reportedly being detained incommunicado. The media crackdown has been seen as largely a measure to curtail further public demonstrations and mobilisation.

Public unrest and the subsequent official clampdown seems to have done little to harm President Omar al Bashir’s international image. As an apparent reward of Bashir’s positive statements on southern independence international sanctions against Sudan are about to be lifted. On Monday the US State Department announced it is initiating the process the process to remove Sudan from the US list of state sponsors of terrorism.

Plans to remove Sudan from the terror list have been met with outrage by human rights groups. Bashir himself is wanted for war crimes by the International Criminal Court for mass killings orchestrated in Sudan’s western Dafur region. Episodes of violence — reportedly state sponsored — continue unchecked in Darfur even as international attention is focused on the peaceful process in the south.