iPad and Converting Movies

Tried to convert a bunch of movies to an ipad format using the preset on Handbrake. when I load them onto my ipad, none of them work. It sees them as video files, gives me how long they are. But them they won't play. Is there a setting I am missing?

EDIT: Could it be a failure in syncing it?

Is there a better video player that isn't so picky in terms of file formats?