What encoding software are you using? I only use camtasia or flixpro or sorenson squeeze. These build in the player as a single file.
flv is notoriously bad for this as (I believe) you can't easily embed the player in the file.
Can you save the file as an swf instead. There really is not that much difference.
Here is a general site I used for settings.
http://www.squidoo.com/youtuberight/
