I've noticed that there is a difference between the packaged version and the .Jar version of the same app, in this case, my B4X-Launcher... Here's the screenshots to better illustrate.
Compiled .jar file graphic result:
Same App, same .Jar file, Packaged into .exe:
So, in order to the resulting .exe version to look good, I've been offsetting the window dimensions by 5px in both Height and Width.
BTW, you should try to create a more flexible layout that automatically adjusts based on the window size. Just set the anchors of the background blue pane to BOTH and it will fill the gap.