Audio Problem on Quicktime Pro/Ipod Classic

I just downloaded Quicktime Pro and followed the steps in order to get a video from my desktop to my ipod classic. It looked and sounded fine on my Itunes (Aside from taking forever to convert). But by the time I had to convert it again for my ipod the picture was subpar and the audio was horrible. Can anyone help me?
Thanks

FCE works best with AIFF audio @48kHz. You can convert mp3s in iTunes (DRM prevents use of many iTunes Store tracks in FCE) but they wind up @44.1kHz. It's better to convert in QTPro, as that can give you the correct sample rate.

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