That happened twice in a row lately...
While we installed last 2 lighttpd servers, we found that most of client videos were not metainjected.
Streming movies with lighttpd won't give you expected effect if there are no information about video keyframes!
There are few more bad things if videos not metainjected, but here we're talking of lighttpd.
Still such videos can be metainjected, online or with desktop tool, but it can be a pain if you have a lot of videos, or videos are long.
So please take this into consideration. Check if your flvtool2 (or yamdi) tool is working well!