I have received updates for Pages & Keynote but it then says that they are not compatible with my iPad at this time.  I assume that when I update to iOS 5 they will then be compatible, I hope...
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Yes, it’s very likely that the Apps that are not compatible are expecting to see the newest version of the operating system. The way it should have been designed is for the updated apps not be allowed to be installed until the required iOS has been updated.