It might be an issue of turning Y’CbCr into RGB.
Color works in RGB color space as does shake.
i.e. if you give it Y’CrCb material it will render in RGB within the application.
Final Cut Pro, on the other hand, works in Y’CrCb color space.
in short: Quicktime movies encoded using an RGB codec (such as Apple Animation) are imported with an automatic gamma adjustment of Aprox. 1.22 into FCP. THE EXACT OPPOSITE happens when you import Y’CbCr codecs into RGB apps, such as Color or Shake.
long story short:
If the image is too dark try a 1.22 gamma shift
If it is too bright try and .824 gamma shift