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Depends on how you're doing it, William.
The program will load the file directly to your iPod if you use Share/Mobile Phones and Players and then select iPod from the options.
You mention synchronizing, which seems to imply that you're using iTunes or other software to transfer the video to your device. If so, that could be a lot of issues, including what format of video you've output from Premiere Elements.
I've never had a problem exporting as DV-AVI into quicktime pro then exporting as ipod from there. I've also captured dvd with MPEGStreamclip (free download) and exported as ipod with no issues. Any other file type itunes has to try and convert.
Can you mention the properties of exported video (Frame size and Frames per second.).Import the video in timeline and right click you can see the video properties.