What's the source of the video? That is, how are you serving it out?
I have html5 m4v files working on iPad from a simple "pubpages" server provided by my institution. But, when I try using a MacMini server with 10.7 server software (https - self generated certificate), I get good desktop results, but no ipad (ios 6).
Also, what html code are you using to call up the video?