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Sorry about the question about the conversion software. I always forget to go back and check the thread title for key information.
I'm not a Pano2VR user so this may not be very helpful but I suspect that what you are seeing is a color management issue. The converter or Quicktime is probably ignoring the AdobeRGB profiles in your images and treating them as either sRGB or monitor colorspace. If you have a wide-gamut monitor, it is possible that the impact could be worse. Here is a thread on the Garden Gnome site that talks about this, although the output in that case is Flash, not QT:
There is a post in that thread that recommends using soft-proofing and converting to sRGB.
If that isn't the problem, my second guess is that Quicktime could be using NTSC video levels. This is where black and white levels are set at 16 and 235 respectively instead of 0 and 255. I doubt this is the problem in this case but maybe. I don't know what you could do about this if it is the problem other than check the Pano2VR settings and see if there is a setting that would allow you to change the behavior.
I don't know if that will help but maybe it will give you some ideas.