I would guess that the color shift is coming from the fact that DV doesn’t use RGB color space. Instead it uses YUV. The shift is probably how FCP translates RGB to YUV.
To test this, create a timeline with the codec set to animation or if you have the AJA codecs installed, use the 10-bit RGB uncompressed codec. Then drop the file into that timeline. Did the color shift?
To get around this shift, I would either take the file into After Effects or Photoshop CS3. Both of those have color management. The new version of Illustrator might have it to, but I don’t know for sure. Change your working color space to YUV.
-Russ
Russell Lasson
Kaleidoscope Pictures
Provo, UT