When the U.S. military overhauled its huge detention center at Afghanistan's Bagram Air Field in 2009, it swore the prison wouldn't be an embarrassment for Washington anymore. But the burning of the Koran at the prison last week, an error that may have jeopardized the entire war, indicates that 10 years of wartime detentions pose problems that cosmetic changes can't resolve.

Military spokespeople rarely say outright that the Koran burning took place at the jail. Official statements more often say instead that it took place at "Bagram" or at an unspecified location in "Parwan," as if the U.S. doesn't want to recognize the connection between what the military calls an accidental incineration and its Afghan mega-prison.

Which is ironic. The detention center is indeed located on Bagram Air Field, although visitors have to be driven to the base's outskirts to view it. But when the U.S. rebooted the prison, it didn't want any verbal associations with Bagram, which had become associated with lawless, opaque detentions and outright torture; you were supposed to call it the Detention Facility in Parwan, for Parwan Province. Subtext: This Is Not Bagram.

The reason was simple. At least two detainees were beaten to death at Bagram in the early years of the war; a documentary was even made about it. More recently, rumors circulated throughout Afghanistan that a secret torture chamber, called the "Black Jail," still existed at Bagram. A former Navy SEAL, Vice Adm. Robert Harward, took charge of overhauling detention operations for Gen. Stanley McChrystal, then the commander of the war, and he concluded he needed a whole new prison to signify a clean break.

So the U.S. spent $60 million building a new wartime jail, opening its doors to its unwilling denizens in late 2009. Its former warden, Brig. Gen. Mark Martins, took me on a tour that August. He took pride in the gardens and sewing machines on the premises where detainees could learn horticultural or tailoring skills that could help them earn a peaceful living. The Detention Facility at Parwan was heavy on communal living, a subtle rebuke of the military's previous reliance on isolating detainees.

It earned praise from some of the critics of the old Bagram jail. The Red Cross said it had "routine" access to detainees at Parwan. Others fretted to me about insufficient due process for the detainees, but considered Parwan an improvement over the old jail.

The U.S. liked the detention center so much, it decided to keep it for a while. Last month, it backed off a plan to turn Parwan to the Afghans, who it said weren't yet ready to run the jail professionally. Then it signed a $35 million contract to expand it massively, building living quarters that can hold 2,000 detainees, double Parwan's current size and dwarfing the approximately 180 detainees at Guantanamo Bay.

That gargantuan size laid bare a truth that cuts against the Obama administration's narrative of a war that's winding down. The longer the U.S. fights in Afghanistan, the more detainees it will have to hold. And running a huge detention center is a complex task, with considerations that stretch far beyond avoiding torture.

One of those considerations may be responsible for the Koran burning. Guards at detention centers typically try to control how inmates communicate. Illicit messages are often suspect. While it's by no means clear yet what actually led to the incineration, one leading theory is that detainees were using Korans from the Parwan prison's library to pass each other notes. That may – repeat: may – have led to guards destroying material from the library; the official explanation thus far is that the guards didn't know the Korans were included in the pile of books and papers slated to go up in smoke.

It'll take the conclusion of the NATO's official investigation to know for sure. On Monday, a spokesman, Navy Capt. John Kirby, told reporters he didn't know when the inquiry would wrap up, although Pentagon reporters were told it would be done by month's end later this week. It's also unclear if the inquiry will recommend any changes to detention operations, in addition to the narrower question of how to dispose of Korans.

The war's commander, Marine Gen. John Allen, has ordered all his troops to undergo re-training in how to handle religious materials with respect. But it may not just be a respect issue. While U.S. troops can certainly exercise common sense about the Koran, the pressures of running a giant military detention center for years to come may not be getting similar scrutiny. If they don't, no amount of rebranding may save the Afganistan war.