Haraz N. Ghanbari, File, Associated Press
FILE - In this July 6, 2009, file photo, President Barack Obama and Russian President Dmitry Medvedev, rear, look on as then-Joint Chiefs Chairman Adm. Michael Mullen, left, and his Russian counterpart sign the Joint Understanding for the START Follow-on Treaty at the Palace of the Kremlin in Moscow. Two-and-a-half years after the Obama administration launched its much-touted effort to patch up relations with the Kremlin, the once-bitter, Cold-War foes are at odds about everything from missile defense and Georgia’s borders to the deployment of Russia’s conventional forces in Europe.

WASHINGTON — The U.S.-Russia "reset" is sputtering.

Two-and-a-half years after the Obama administration launched its much-touted effort to patch up relations with the Kremlin, the once-bitter Cold War foes are at odds about everything from missile defense and Georgia's borders to the deployment of Russia's conventional forces in Europe.

Cooperation is similarly strained in areas that have weathered the worst breakdowns in recent relations between Washington and Moscow, raising worries over U.S. supply routes to Afghanistan and the international alliance against Iran's nuclear program.

The widening divide between the United States and Russia is occurring as the former communist power undergoes a complicated transition, with Prime Minister Vladimir Putin preparing for his likely return to the presidency and the government struggling to deal with anger sparked by evidence of election fraud and manifested in the country's largest protests since the collapse of the Soviet Union.

If Russia's government has been weakened domestically, it is still talking tough internationally. And its adoption of an increasingly harder line in recent weeks has created several diplomatic headaches for the U.S.

The crowning achievement of President Barack Obama's reset policy occurred in February, when a U.S.-Russian agreement to reduce their nuclear weapons arsenals entered into force. Senate ratification only came after difficult negotiations and over the objections of several leading Republicans, who challenged whether Moscow would adhere to the treaty or use it to challenge unconnected American military programs.

Some feel those fears are now being validated. Even though the "New START" treaty doesn't significantly limit U.S. missile defense plans, President Dmitry Medvedev has threatened to pull Russia out of the accord if the U.S. moves forward with plans to place missile interceptors in Europe. He has also ordered Russia's military to ensure capability to destroy the system's command structure, and warned of stationing strike missiles in the Kaliningrad exclave between NATO allies Poland and Lithuania.

"After being assured that the New START treaty would contribute to the improvement of U.S.-Russia relations, and that the Russian government would not use the treaty against us as blackmail, we are now in a situation where the president of Russia is threatening to deploy ballistic missiles to destroy U.S. missile defense systems in Europe," Sen. John McCain, R-Ariz., lamented before the Senate last week.

McCain also decried Russian attempts to reach out to China and Iran to deepen cooperation against U.S. missile defense plans, and threats to cut off supply routes that are critical for NATO's mission in Afghanistan.

Administration officials concede that they are unsettled by Russia's behavior, but there is little they can do right now. The populist passions of the Russian election season increase the danger of exacerbating disagreements that may only reflect rhetorical bluster.

On Tuesday, Russian Foreign Minister Sergey Lavrov angrily accused the West of taking an "immoral" stance toward Syria by pressuring President Bashar Assad while refusing to condemn the "armed extremist groups" trying to oust the Arab strongman. His language echoed the widely discredited claims of Assad, whose government is accused of killing more than 5,000 people in a brutal crackdown on primarily peaceful dissenters.

U.S. officials described Lavrov's comments as "baffling" and "unhelpful," but they may be more destructive than that. As a veto-wielding member of the U.N. Security Council, Russia continues to stand in the way of any effort at the global body to condemn Assad's regime and set multilateral sanctions. With the help of China, Russia has already blocked one resolution against Syria and has continued to supply the Assad regime with weapons.

A similar situation exists with Iran. The U.N. nuclear agency revealed secret Iranian experiments whose sole purpose is the development of nuclear weapons — the strongest rejection yet of Tehran's argument that its uranium enrichment activity is purely for energy production. But Russia, which has deep trade and investment ties with Iran, has shielded the Islamic republic from any new global sanctions.

The U.S. sees a growing Russian unwillingness to cooperate seeping into other areas as well. The Obama administration grew so frustrated with Russia's role in the Middle East process in September that it toyed with the idea of disbanding the "Quartet" of Israeli-Palestinian mediators, which also includes the European Union and the U.N.

And Washington finally grew fed up with Moscow's refusal to provide information on its conventional forces in Europe — as required under a 21-year agreement with the West — that it decided last month to no longer share its data in return. Talks have likewise stalled on other elements of a once ambitious U.S.-Russia arms control agenda.

The relationship isn't all bleak and certainly hasn't reached the low point set after the Georgia-Russia war in 2008, when George W. Bush was president.

Russia will enter the World Trade Organization in early 2012, ending an 18-year pursuit that had partly been stymied by several U.S.-Russian commercial disagreements the Obama administration pushed to resolve. Moscow's accession was sealed when Georgia — with U.S. encouragement — withdrew its objections.

Ultimately, how Russia responds to its internal strife could be the most decisive factor in determining the long-term trajectory of its relationship with the U.S. If it blames Washington for the unrest or flagrantly violates the rights of Russia's citizens, a skeptical Congress would demand a tough response from the administration. Many Republicans openly deride the reset policy already.

Shaken by the public anger, Putin's initial reaction was troubling. He accused Secretary of State Hillary Rodham Clinton of instigating protesters to weaken Russia and warned that his government wouldn't tolerate foreign interference.

But there was no violent crackdown on demonstrators. Three days later Medvedev announced an investigation into claims of voter manipulation. And officials refrained from pointing the finger at the U.S. again.

"Russia has one of the most highly educated populations in the world and now a growing middle class, with all the aspirations that middle-class families have," Clinton said Wednesday at an event focusing on American innovation and trade. "This didn't come from the outside. It came from within."

Associated Press writer Desmond Butler contributed to this report.