I know, that's a shaky source, but according to this article (emphasis added):

WASHINGTON, May 25 - Newly released documents show that detainees at Guant�namo Bay, Cuba, complained repeatedly to F.B.I. agents about disrespectful handling of the Koran by military personnel and, in one case in 2002, said they had flushed a Koran down a toilet.

U.S. 'Thumbs Its Nose' at Rights, Amnesty Says (May 26, 2005) The prisoners' accounts are described by the agents in detailed summaries of interrogations at Guant�namo in 2002 and 2003. The documents were among more than 300 pages turned over by the F.B.I. to the American Civil Liberties Union in recent days and publicly disclosed Wednesday.

Unlike F.B.I. documents previously disclosed in a lawsuit brought by the civil liberties union, in which agents reported that they had witnessed harsh and possibly illegal interrogation techniques, the new documents do not say the F.B.I. agents witnessed the episodes themselves. Rather, they are accounts of unsubstantiated accusations made by the prisoners during interrogation.

On Wednesday, the Pentagon dismissed the reports as containing no new evidence that abuses of the Koran had actually occurred and said that on May 14 military investigators had interviewed the prisoner who mentioned the toilet episode to the F.B.I. and that he was not able to substantiate the charge.

The accusation that soldiers had put a Koran in a toilet, which has been made by former and current inmates over the past two years, stirred violence this month that killed at least 17 people in Muslim countries after Newsweek magazine reported that a military investigation was expected to confirm that the incident had in fact occurred.

Newsweek retracted the report last week, saying it had relied on an American government official who had incomplete knowledge of the situation.

None of the documents released Wednesday indicate any such confirmation that the incident took place.