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Actually, the 1.0.1 update with a number of WebDAV fixes is still not available (unless the App Store is giving me stale data).

People have been reporting that iTunes is telling them that there are updates to apps which haven't actually been updated, and in fact I'm seeing this too (iTunes is telling me I have two updates, then shows me a list of 11 supposedly-updated apps, none of which are actually updated). Any chance this is what has happened to you?