I'm pretty positive that an MP4 file with H264 encoding is NOT a Flash format. It is supported in Flash Player but it is not a Flash format. Flash-specific formats would be F4V and FLV.
See the blog post on InDesignSecrets.com I did on video formats in June 2011. As far as I know, nothing has changed since then:
http://indesignsecrets.com/picking-the-best-video-format-for-digital-p ublishing.php