Yeah, it’s a really funny one this.
The NetStream method doesn’t care what the files are called (inc. the extension), but the flvplayback component (which ships with adobe cs3 and is often used to play flv files) prefers files to end with ‘.flv’.
The relevant quote:
“All your existing video playback front ends will work as they are. As long as they do not look at the file extension that is, though renaming the files to use the .flv file extension might help your component. The Flash Player itself does not care about file extensions, you can feed it .txt files for all it matters. The Flash Player always looks inside the file to determine what type of file it is.”
I found that renaming my h.264 files from .mov (e.g. quicktime) to .flv was all it took to get them to play.