Compiling executable on OS X removes menu bar?

Hello, I recently upgraded to R2012 on Mac OS X 10.6.8 and compiled a gui program that I have used for several years on previous versions. It runs fine from the matlab window (uncompiled), but when I run the compiled version, the menu bar is missing from the main figure window! It is a custom menu bar created with guide. Anyone have any thoughts? Thanks!

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Is it up at the top of the screen (that shared menu bar space that most apps use) on your Mac?

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