While it might be a difference in the diapers, I'm betting it is the extra amount of time with a wet diaper. We have always used Desitin (like pp said, original, not creamy or clear) overnight to protect their skin when they started sleeping longer (every night, not only when they have a rash).
Also, to help clear up a diaper rash once it starts (teething, etc.), we put Desitin on and then put baby powder on top of that as an extra barrier. Works great.