I know I had a similar problem getting movies to work with firefly…had absolutely NO luck exporting from quicktime pro.
I now use “visual Hub” to export to Itunes/mp4 as it has presets for the likes of ipod video, apple TV, etc and its fast. Still cant play video through Itunes but choosing “source” from the frontrow menu and choosing my daap share, I can access the movies and music and the .mp4 files WILL play through frontrow!
I dont know if it makes much of a difference, but I have specific movies and music folders set up and set up the firefly server to look at both folders.