I have had good success with ffmpeg and real media so far. Is ffmpeg fully encoding the video? What codec are you encoding it into? ffmpeg includes a few different encoders and I believe only the mplayer encoder will correctly handle real media. Finally, what are you trying to play the encoded video with? If you are encoding it as an avi file and trying to play it with Quicktime, that may be your problem. Will it play in VLC?