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No, your source file makes no difference whatsoever; only the final version that PocketMVP plays.
Which Axim do you have? Mine is the Advanced (ie. 400Mhz) and I only have audio sync issues on landscape video, which is why I switch to Lame stereo to keep them in sync. My portrait videos, I can keep in mono with the Fraunhofer codec, and so far they stay in sync just fine.
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