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My video uploads are transcoded to flv, mp4, ogg and webm.
In theme_video_formatter_player the formatter uses the extension of the first file ($item['playablefiles']->uri) to determine whether to use video_play_flv or video_play_html5.
Since the first of the 4 files is always the flv, I only get the flash player (Flowplayer in my case) and never the html5 player.
Of course when I change the player for flv files to html5 (video for everybody) then the html5 theme function is always used and there is never a flash player.