I only get my smaller vids converted - say about 2 megs - anything above that the process queue just says 'downloading' forever.
If that's what you get, then just go to the vid folder in ftp (the one that gets the download) copy the name of the file and pop it into the process_queue table in phpmyadmin - then change status to 2 (once you're sure its all downloaded of course).

When the cron runs next it'll convert.
It's fast once you get used to it and its a quick workaround
Another workaround which is messier is to paste in just the link from the embed code to a browser - when its returned the file name is changed - then you change all of the swf/swf? crap to 'get_video' and plug that into the file name in process queue phpmyadmin.
same result cause you're using utubes own code to do it.