Compressing for Apple TV

I have a question for you video compression gurus out there: I am living in Norway, and we always make video in 25 fps (PAL) or 25 fps/50 fps (HD). I have created several animations with the excellent software ArtMaticPro (from U&I Software), and I have chosen the format 1280x720 25 fps with no compression (Animation). - And here is my question: When I compress these animations with either Compressor, QuickTimePro or VisualHUB to MPEG4 H.264 25 fps, some of the animations are stuttering. If I open the compressed MPEG4 file in QuickTime and use the cursor to move one frame ahead at a time, I can see that the same image has been used in two continuos frames a few places. When I play back the H.264 file on the AppleTV, this freezing effect is very visible and of course irritating! I have to mention that I have set the max datastream below 5 mbps (as is required), and there is absolutely no timecompression used.
In Apple's podasttechspecs it is stated that the format for the AppleTV should be 960x540 and 30 fps when the source video is 1280x720 and 30 fps. There is no specs for my source video (1280x720 25 fps). - What should I choose? 960x540 and 25 fps? Someone suggested that I should keep the frame rate no higher than 24 fps, but I don't understand this argument.
What I am really looking for, is a professional guide that I can use in order to get the most out of the source material (1280x720 25 fps Animation) when converting to HD and the AppleTV.
Any help is very welcome!

Thanks for the reply! So what you are saying is that the AppleTV is designed to play back 960x540 when the frame rate is 25 fps (like it is on my videos)? I'll try that.
However, the problem must be in the conversion process. My problem goes a little deeper, because I need to convert my animations videos before I import them into FinalCutPro6. FCP6 is not able to play back video in Animation (no compression). Most them are not even visible in FCP6 (only black image in both Browser and Canvas). However, if I play them back in QuickTimePro, they play perfectly for three-four seconds, then the data rate is obviously too big for my MacBookPro 2.33 Intel Core 2 Duo with 3 Gbyte RAM, and the image will freeze. - I am looking for a method to convert from Animation to a compressed format that I can use in FCP6 without loosing too much of the quality. Any suggestion?

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T-Bob wrote:
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Thanks Tom. Could be just my eyes seeing the difference in the results, but here are the details.
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Encoding Mode” multi-pass
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