Thank you particularly for the arstechnica.com link. The way I read the discussion before, I was expecting the conflict to be originating with Apple (like something in their agreement forbidding the use of GPL'd software or something). But after reading that article I see that it is the FSF that has pointed out how Apple's App Store restrictions make apps using GPL licensed software out of compliance with the GPL. That makes more sense.
More recently, this line of argumentation was used by a VLC contributor to pull a VLC port off the App Store by citing copyright infringement: http://www.readwriteweb.com/archives/as_vlc_for_iphone_ipad_...