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Application window minimized after stop

I have a typical state machine that I use as the base for almost everything I do. Now recently I made a major change to about 90 of the 500 vi's that it uses.  Everything works fine except once I have compiled it into an executable it dose something odd.  When I hit stop the application minimizes itself instead of just displaying the run button.  The minimized application cant be resized or started again. I am running LV8.6
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Does the same thing happen when you run it as a VI?  If not you might just consider rebuilding the application.  Also what are you actually doing in your code to close your VI?
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