Hi,
I see there were a lot of posts regarding the symptoms of my problem, but I couldn't really find any answers. The issue I am having is with videos encoded using mpeg-4, yuv420 (?) . The player plays the audio fine, but I cannot see any video.
This is the ffmpeg output for the mpeg-4 video:
Stream #0.0(und): Video: mpeg4, yuv420p, 320x240 [PAR 1:1 DAR 4:3], 15 tbr, 15 tbn, 15 tbc
Any help would be much appreciated.

Even though there are several places that say otherwise on this site, Flash cannot play old mpeg-4 encoded video. It can play H.264 encoded video which is encapsulated in an MP4 file, but this is not the same thing.
http://en.wikipedia.org/wiki/Mpeg-4
http://en.wikipedia.org/wiki/H.264
http://en.wikipedia.org/wiki/Flv#File_formats