Sorry to hear ffmpeg isn't working for you. I mostly use it to convert avi but have converted wmv1 and wmv2. Have noticed some conversions have come out 'blocky'(my best technical term).
Have you tried altering the frame rate or bitrate, or trying 2 passes?
Maybe if you describe your video problem a little more clearly one of the video wizards will have an answer. Sorry I can't be more help