You could try adding SDL_WINDOW_BORDERLESS to the flags. Also make sure you're using the latest head revision from the Mercurial repository. SDL 2.0 is certainly a work in progress; I remember they committed just recently some fixes to Linux fullscreen mode. As far as I'm aware SDL 2.0 is trying to be friendlier with the window managers and their various extensions, however that also makes fullscreen mode setup more errorprone.
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