Optimizing moves a section of metadata information called the moov atom, from the end of the file to the beginning. The moov atom contains the information the unit needs to start playing the movie. So when it's at the end, the unit has to load the whole movie before it gets the information it needs to start playing. Moving it to the beginning provides the unit with the needed info right away. So it will start playing once enough of the movie has buffered.
Sounds all good...right? Why would anyone not want the moov atom at the beginning? Well, moving it to the beginning means if there is any changes to the metadata, all of the file needs to be re-written. When it's at the end, the file does not have to be re-written if there are metadata modifications. You will notice this mostly in iTunes. If you edit your metadata in iTunes, you will notice it will be slower (spinning beach ball) to accept your changes. I recommend editing metadata in Subler, not iTunes. Subler does a quick job of re-writing the file. Then you go into iTunes, select the movie you have modified, do a Get Info, and it will quickly update your changes.