According to the New York Times:
An American military inquiry has uncovered five instances in which guards or interrogators at the Guantánamo Bay detention facility in Cuba mishandled the Koran, but found “no credible evidence” to substantiate claims that it was ever flushed down a toilet, the chief of the investigation said on Thursday.
All but one of the five incidents appear to have taken place before January 2003. In three cases, the mishandling of the Koran appears to have been deliberate, and in two it was accidental or unintentional, the commander said, adding that four cases involved guards, and one an interrogator. Two service members have been punished for their conduct, one recently.
I am not sure if the service members that were punished had other things to answer for- the investigation is by no means complete, apparently.
However, I am curious if that was what they were punished for. Does the Koran have some special legal protection in the United States now?