That definitely sounds like an upgrade issue. This used to happen with the FCP4.5-FCP5 upgrade. Are you on the latest version of QuickTime?
Try starting a fresh project file in FCP6 and re-copying the sequences and clips over, see if it makes a difference. It's unlikely that your actual media files have been tampered with; it's probably just the way FCP interacts with them. I doubt you would have to recapture any media.
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