Different Behavior when Closing a Standalone Application

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I'm experiencing two different behaviors with a standalone application generated in R2012a for deployment on Mac computers. If I quit the application by pressing Command+Q, or on the Apple toolbar selecting Quit from the application name menu item the MCR_CACHE directory is maintained, however; if I click the red circle button on the GUI's window the MCR_CACHE directory is destroyed. This is of great concern for me because users are able to manipulate MAT files within the application to customize it for their needs, but the moment they click the red circle exit button rather than pressing Command+Q or selecting Quit from the drop down menu they've loose all that customization. What's going on here, and how do I fix it?
Also, I've noticed that the toolbar I created for my GUI application within GUIDE will appear above the application when I run it on my computer, but on other computers will appear on the Apple toolbar at the top of the display. This is a much less pressing matter, just cosmetic really, but I was wondering if anyone knew why this is happening.
Thanks, B

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Bruno
Bruno 2013-5-5
So, the workaround for this issue is to call "exit" from the close request function if deployed.

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