This is not just H.264, This is Apple TV compatible H.264

I bought an Apple TV hoping to use it as a viewing station for content previously webcast and recorded using QuickTime Broadcaster.
After the webcast I took the resulting H.264 file which QTB recorded during the webcast and dropped it into Itunes which synced it to the Apple TV.
It looks awful on the Apple TV. Huge artifacts, colour distortion and horizontal tracing reminiscent of insufficient key frame information or something similar.
Interestingly tho, when you shuttle through the file on the Apple TV in FF or REW each frame displayed looks perfect. ??
I had assumed because I was recording a native H.264 video file from within QTB that it would transfer directly to Apple TV and play no problem. The frame size, frame rate and data rate are all within Apple TV specs.
Play it back in QuickTime player and it looks beautiful.
Apparently not all H.264 files are the same. having done some subsequent reading there are apparently different profiles of H.264. Baseline, Main (CAVLC) etc.
I'm not sure what this all means tho'
Of course, I could convert them using one of the Apple TV converters but that defeats the purpose of recording native H.264 in the first place. Besides I don't fancy the rendering time of re-encoding 50 real time hours worth of video for the benefit of the Apple TV. I'd be as well getting a Mac Mini and use Front Row.
Can anyone offer an explanation as to why the QTB files would not play properly on the Apple TV?
This is a real shame.
Macbook core duo, Imac 24",Macmini Mac OS X (10.4.8)

It could be a b-frame issue.

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This is not just H.264, This is Apple TV compatible H.264

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