Sub-application Glitch?

I have a frame with all my interface buttons on it, and it contains a Sub-Application that loads the rest of the frames in the program.

My frame has two layers, the bottom one has the sub-app, and the top one has the interface buttons, some of which overlap the sub-app window. Everything looks right in the editor, but when I run it, the buttons go beneath the sub-app, even though they are on a higher layer. Is there a way around this? Is this a bug?

What is the best way to create a menu that you want to appear over many frames? If I decide to tweak the interface, I don't want to have to adjust all 20 frames of my program.

Thanks...
Andy