Informed Comment just linked to an article from late December that I think is important to note. It addresses the way the pentagon has ignored Obama in his attempts to close Guantanamo. You can read that report here.
Of course that is only a piece of the puzzle, much of the blame for failing to close Guantanamo rests with President Obama himself. He was too inexperienced to know how to deal with the military and unfortunately our military has been emboldened by his lackluster performance as commander in chief. The article where I found the link to this story discusses some of the other troubling issues in regards to the U.S. military's continued disregard for its civilian authority. The bottom line is that the military does what it pleases and we give them most of our tax dollars without any real oversight.