Does the VIN on the sticker match the real VIN of the truck?
It's my understanding that the stickers are put on as the truck comes off the line, and is tied into the manufacturing process. So if the truck is supposed to have, say, a sunroof, and you ordered it deleted, it shows on the sticker, or if you added say a different rear end, it would be on the sticker.
In essence, there's NO WAY this should be wrong, especially with something as basic as a body style. We're not talking interchangeable radios or wheels here.
Maybe it was not the window sticker, but the computer build record of the VIN, and I believe that can be altered after the fact, to accommodate such things as dealer-fit accessories. Then again, show me a dealer who can make a QC into a CC!