I have made pita twice recently, both times it stayed puffed after baking. I know when I have bought it from the store it was flat.
It tastes great, it is just difficult to store.
Maybe try cooking it for slightly less time.
EDIT: Also when you're done cooking it, wrap it in a towel. When you cook more, wrap it in the same towel. This will help to soften the crust through a steaming process.