The toolbar at the top is actually a separate window, and it has a habit of appearing when not wanted over top of a full-screen ("kiosk" mode) app. For example, if you ShowDialog
a second full-screen window from the first, the Start window flickers up for a split second before going away.
The only way I ever found of dealing with it was to hack into the API and actually make the Start window hidden while my application was open. This is a big potential problem, because if your app crashes without making the Start window visible again, it will stay invisible until you reset the device (or run you app again successfully).
I'd advice against doing this unless you absolutely have to. As ctacke
points out, this would be an example of an app not playing nicely with Windows Mobile.