I just wanted to note that this is still a problem. I just tried to watch the most recent HD-MP4 episode of going deep on drawbridge.
If I try to watch it on my mac (2011 Macbook Pro - 10.7.2) in Quicktime X then every few seconds the video becomes garbled (gray blocks). If I watch it in VLC then those some time points where it is garbled in Quicktime X are instead rendered as a stutter in the video. However if it is played in Quicktime 7 player then it plays fine.
So It would be great if you guys could fix this so that the video files play fine on iOS devices as well as macs. But in the meantime mac users can install Quicktime 7 on Snow Leopard or Lion to view the MP4 files properly.