Videos Converted, but wont sync

I own a 60 GB iPod Video. I love it--I think the video quality is stunning, and I absolutely love the ability to plug it into a TV anywhere and view whatever I want.
Copying my DVD collection using HandBrake to my iPod was a breeze (besides the time commitment). It works great, and I love that I'm now carrying that collection in my pocket.
I've had a lot of success converting movies from DiVX (.avi) to iPod Video using Quicktime Pro 7.0.3, but I've also encountered one oddity:
Occasionally I will import a video that I've just converted using QT Pro into iTunes, and, although it plays in iTunes, it gives me the generic message that it is not supported on the iPod. I know that it is the same format (initially as well as after the conversion) as the other files I'm applying the conversion to.
Has anyone else encountered this problem?

Crashing does sound unusual. However, be advised that even if you are able to convert and save a file, there will not be any audio track on the new file. Muxed audio/video file types (MPEG1, MPEG2, VOB, etc.) require a third party application that first extracts the audio and video data and creates and intermediate file containing separate audio and video tracks which QT Pro (or a QT tools based application) can then convert to your target file type.

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