H264 Stutter problems

Um, I posted this in the wrong (Mac) forum, so forgive the cross post.
I'm trying to figure this out and hope someone here can save me hours of experimentation.
I've noticed that, in particular, high quality videos (640x480) at 4:3 aspect ratio using H264, 29.97fps and a bit rate of 1700 or so will "stutter" when I play them back either using the computer or Apple TV. It's not horrible, but it's a definite difference from the smooth playback I can get with widescreen videos.
Does anyone have a clue as to what is happening? Right now I'm experimenting with higher datarates (2200) and after that I'll go to the opposite extreme, but perhaps there are some other settings I'm missing. Other than the stuttering the overall quality of image and sound is superb, but I feel like there must be a simple thing I'm overlooking here.

As others have said you really should keep the original in case you need to re-encode. Unfortunately without the original you don't even know if it might be the original that's stuttering, though frame rate change would crtainly cause issues.
The stuttering might be AppleTv (especially if Visualhub 'Go Nuts' uses parameters that AppleTV struggles with - download MediaInfo and see if the file has CABAC set, AppleTV doesn't support this). Unfortunately there are countless possible encoding options for h264, and some will make AppleTV choke because they are too processor intensive.
I'd also add that different encoders can be really fickle. I generally quite like Handbrake for simplicity, but I tried to convert a PVR recording using it and there were audio glitches all over the place - tried MPEGStreamclip on same source and no issues at all. There are far too many factors for use mere mortals to consider.

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