The moral bankruptcy of the legal system is due to the static legal enforcement... The key is leadership. We often face the belief that the president shouldn’t be involved in law enforcement. But in my opinion, the president should be involved in law enforcement but not the court process. Law enforcement is, indeed, the president’s duty.
Basically, the judiciary is accusing SBY of a lack of leadership - harsh words from the Third branch.
Despite having just a five-year term, Chief Justice Mahfud has been quite outspoken and sometimes critical of the other branches of government. Some Indonesians seem to believe the House's recent "reforms" to the Constitutional Court were a sort of retribution against an activist and outspoken court. On the other hand, if the House and president don't like the chief justice, they only need to wait a few more years to replace him. How much of a role is personal politics playing? It's always difficult to tell in these situations, but in Indonesia personal politics can never be entirely discounted.