I had Wowza RTSP playback problems in Safari and QuickTime for Snow Leopard too when using the Apple H.264 codec:
I find it interesting that you say Lion clears it up -- I will have to try that again when I get a chance.
I would recommend not using the Apple H.264 codec wherever possible. In your case, you could re-encode using ffmpeg pretty easily. You could use the commands at the link Richard provided, or you could just grab the binary here and try your own commands:
Something like the following should work:
ffmpeg -i /path/to/inputfile.mov -vcodec libx264 -b:v 1500k -acodec aac -strict experimental -ar 44100 -ab 128k /path/to/outputfile.mp4