Will Sudan's agonies ever end? Last year, the people of South Sudan voted for statehood with the north's apparent blessing, raising hopes that both sides had put the worst of their past behind them. Celebrities everywhere cheered. But now Khartoum's jets are bombing South Sudanese towns and even a U.N. compound, and Sudanese dictator Omar Hassan al-Bashir is threatening to "liberate" the south from its elected government.

Something's gone badly wrong. Maybe President Obama's new Atrocities Prevention Board can convene a study group.

The supposed cause of the fighting stems from the usual combustible mix of unsettled borders and disputed resources. In 2005, the Bush Administration helped negotiate a "Comprehensive Peace Agreement" that ended the 22-year Second Sudanese Civil War. But the pact failed to draw a definitive border between north and south. Instead, it left the status of several key frontier provinces—some of them rich in oil—to be settled in the future by referendum and "popular consultations."

Things didn't work out as planned. The status of the border areas was still in dispute last year when South Sudan became independent. North and south never could agree on a revenue sharing plan for their oil, more than half of which is extracted in the south and then delivered to market via refineries in the north.

In January the government of South Sudan began shutting down northbound shipments, accusing Khartoum of stealing millions worth of crude. The south also signed an agreement with Nairobi to build a pipeline through neighboring Kenya. Last month, South Sudanese forces seized control of oil fields in one of the disputed areas. Khartoum re-took the oil fields last week and launched bombing raids "deep into South Sudan," according the Susan Rice, the U.S. Ambassador to the United Nations. The old civil war has resumed, only this time it's a war between states.

No doubt there's a case to be made that all this might have been avoided if only the peace accord had been better drafted. Or maybe there wouldn't have been a peace deal at all if the accord had been any more specific.

But that misses the point. The source of Sudan's woes isn't about borders or resources: It's about the continued reign of Mr. Bashir and his Islamist National Congress Party, which has been in power since a 1989 coup.

Successive U.S. Administrations have dealt with Mr. Bashir as they have with North Korea—through a predictable combination of rhetorical denunciation and diplomatic overtures. Mr. Bashir has been canny enough to toy with foreign intermediaries enough to stave off any real consequences to his regime. During last decade's Darfur crisis, for instance, President Bush came near to imposing a no-fly zone on Sudan, only to be dissuaded from doing so by U.N. Secretary General Ban Ki Moon.

Mr. Obama's record on Sudan has been worse. As a Senator he was vocal on Darfur and in 2009 said he was "fully supportive" of the International Criminal Court's indictment of Mr. Bashir on five counts of crimes against humanity. In practice, however, the Administration has been nothing but conciliatory toward the regime, a piece of its broader philosophy of engagement.

"The decision by the ICC to accuse Sudanese president Omar al-Bashir will make my mission more difficult and challenging," J. Scott Gration, the Administration's special envoy to Sudan, said in 2010. He added that "resolving the crisis in Darfur and [the] south, issues of oil and combating terrorism 100 percent, we need Bashir." U.S. diplomats used to say similar things about Serbia's Slobodan Milosevic, Syria's Bashar Assad, and the PLO's Yasser Arafat.

Now Mr. Obama is calling for Khartoum to end its bombing and for the two sides "to return to the table and negotiate and resolve these issues peacefully." Good luck with that. Sudan's agonies will endure so long as Omar Bashir remains in power, with America's quiet acquiescence.