Hello Stevi,
You should probably check your VI Properties for window size. First, make sure your front panel is sized exactly how you want it to appear. Then go to File >> VI Properties, and select Window Size from the drop-down box. Click on the "Set to Current Window Size" button. Also select "Maintain Proportions of Window for different monitor resolutions". These two selections should ensure that the VI and/or EXE will run with the desired window settings.
Hope this helps!
Liz Fausak
National Instruments