Lines like the following in flashvideo_get_flashvars make the assumption that the thumb is where flashvideo put it. 

$video['flashvars']['image'] = check_url(preg_replace("/\.flv|\.mp4/", ".jpg", $video['file']));

Filefield_paths module allows me to move files to other paths based on tokens, and it correctly updates the files table and node when it does this. Flashvideo should be looking on the node.