Screen size problem difference in test and installed

I have a strange problem with the screen size on an application I am making. The Images are attached.

On the test in CS5 I get the correct layout, and the navigation bar and scoring is at the bottom. However when I publish and install the application I get the nav bar and score moved up. The reason is that the screen size is changed and I use the hight and subtract the y co-ord from the bottom. The screen dimensions are 666w 984h in test and change to 652h 994w. Any idea why?

Test image from CS5

Published application