Problems With MPEG-2 Codec

I've been having problems with Apple's MPEG-2 codec for Quicktime.
All my 640x480 movies are labeled as 720x480, and when I convert them to .mp4 with VisualHub (third party software) it stretches them to 720x480. It didn't do this before I got the codec.
Is there any way to fix this?
Alternatively, how do I uninstall the codec?
Thanks.

I am using the Sony HVR-Z1U camera. I have firewire connection on the camera that I have connected a Sony HVR-MRC1K memory  recording unit to. The tape in camera starts the recording then the digital recording kicks on. I have to always have a tape in camera to start recording onto firewire connect digital hard drive recorder. As I mentioned in my previous post, the HVR-MRC1K records to a 32 gb compact flash high speed card and saves files as M2T files (MPEG2) I covert/transcode the files using Clip Wrap software to Quicktime .MOV files. I am them able to import them into FCP X and or iMovie. Once in FCP X the files play, but will skip or drop frames. Again there is no issue on my other mac using FCP 7. I don't even have to transcode files in Clip Wrap. They import automatically using a connected USB drive and Compact Flash Card. I really would like to use FCP X and move forward and not have to take a step backward using only FCP 7. I am in Fort Myers Florida. There is an Apple store nearby in Estero, Florida and one a little further in Naples Florida. I have only gone to the Estero Florida store. The Naples store had FCP classes only twice a week and the Estero store had none.

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