It's a documented "feature" in QuickTime. I'm not sure why it gets set wrong but recently I was handed some footage and only after editing did I happen to notice the size shown was wrong. In fact Apple recently monkeyed with this setting.
What's going on is that QuickTime 7's "Conform aperture to" setting is set incorrectly. It's likely set to "Clean" rather than "Production". (Personally I think it should default to Production but that's me). However Apple believes differently:
Note: QuickTime Player in Mac OS X v10.6 always displays movies using the Clean aperture mode."The main reason I don't like this is because it tends to crop the image and for production that means seeing someone clear the frame or not clearing it…by pixels. From an editing standpoint, things like this affect the timing of the edit which in turn affects the mood of the edit so it's not just me expostulating for no reason.
What to do?
Open the QuickTime clip in QuickTime 7 and hit Command + J for "Show Movie Properties", then click on "Presentation" then at the bottom of the window look for "Conform aperture to:"
Checkmark it if it's not already, then set the pull-down to "Production".
I'm still looking for a way to do this to a multitude of clips simultaneously reliably.