Obama 'has faith' in Gen. Allen despite scandal probe The top U.S. general in Afghanistan is now under investigation, in a case that's linked to the scandal that forced CIA Director David Petraeus to step down. November 13, 2012, 12:20 p.m. President Obama stands by Gen. John Allen in spite of thousands of possibly inappropriate email exchanges, according to White House Press Secretary Jay Carney. Allen's uncovered messages have placed his nomination for Supreme Allied Commander Europe on hold, prompting a Department of Defense investigation. "He has faith in Gen. Allen," Carney said, affirming that Allen will remain the U.S. commander in Afghanistan for the time being. Carney addressed the spiraling series of events that followed the unveiling of former CIA Director David Petraeus" affair with his biographer, Paula Broadwell. The 20,000 to 30,000 pages of emails in question tied Allen to Jill Kelley, a 37-year-old who has served as a social liaison at MacDill Air Force Base in Florida, where the U.S. Central Command is headquartered. Kelley's complaints of harassment to the FBI earlier this year led the bureau to Broadwell, who reportedly was accusing Kelley of seeking romantic involvement with Petraeus. The revelation that Petraeus, who had been scheduled to testify Thursday before the Senate Intelligence Committee on the attack on the U.S. consulate in Benghazi, Libya, had embarked on a relationship with Broadwell that led to his resignation Friday. "This was a personal indiscretion as far as we know," House Minority Leader Nancy Pelosi said Tuesday, adding that there is not yet any evidence to suggest that Petraeus" actions posed a risk to national security. "The president was certainly surprised when he was informed about the situation regarding Gen. Petraeus ... his thoughts and prayers go out to both Gen. Petraeus and Holly Petraeus," Carney said, adding that he was in no way suggesting that Obama was pleased with the week's events. Carney added that it was "a fact" that the White House was informed of Petraeus" affair the day following the election, despite the FBI's discovery of the infidelity over the summer, dismissing accusations that the administration's timeline is suspicious.