Don't forget, the phone doesn't actually know whether or not the flaps are closed. It can't physically tell one way or the other, the pop ups are just a simple reminder, my Z used to give me them all the time, then they stopped one day and never came back.
If it's broke, use a hammer. If that fails, you're not using a big enough hammer.
XDA Developers was founded by developers, for developers. It is now a valuable resource for people who want to make the most of their mobile devices, from customizing the look and feel to adding new functionality. Are you a developer?