On February 20th the government filed a response to an earlier order by Judge Bates (D.C. District) in which Judge Bates invited the government to refine its position as to whether U.S. courts have the power to entertain habeas petitions from detainees held at Bagram Air Base in Afghanistan. The government's two sentence response retained the current position (originally articulated by the Bush administration) which is that U.S. courts don't have jurisdiction to hear habeas petitions from those held at Bagram. SCOTUSblog has a more detailed discussion here.
Why allow courts to hear habeas petitions from those held at Gitmo, but not Bagram? I think an important difference exists, and that is that Bagram is a base in a war zone. But don't the same concerns exist with detainees at Bagram and Gitmo? Both hold prisoners captured in the "War on Terror." An integral part of the Court's decision in Boumediene was that Gitmo is under de facto control by the United States. I would argue that Bagram is under as much control. It is a U.S. controlled military base in a country that is under U.S. military control. Even though there are fundamental similarities between Bagram and Gitmo, I do think the fact that Bagram is a war time base is an important distinction. It should be considered separately from Gitmo, but the reasons for allowing habeas review for Gitmo detainees exist with respect to Bagram detainees.
This doesn't necessarily mean that the new Obama administration is permanently adopting the Bush administration's stance on Bagram. I think the new administration is still trying to get its head around the detainee situation it inherited and is taking some time to carefully craft its policies. We may not see a voluntary change in the position as to detainees at Bagram, but I believe that it is too early to know what the new administration's policies will look like long term.