My guess is that because The App Store puts itself into the Apple Menu, Fruit Menu's changing of the Apple Menu causes a conflict.  As far as my experience The App Store and Fruit Menu are the only programs that change the Apple Menu.
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"I hate all operating systems equally, but some I hate more equally than others."
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Michael Logue                                The Grateful Union
http://www.earthguild.com/    Earth Guild: Tools Materials Books
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