Wolfgang,
This is the procedure I would follow:
The sequence could vary depending on whether you shot raw frames (still with the Bayer pattern) or if you have frames the camera deBayered for you (probably jpg). The former is preferred.
But for now, just go through your normal preprocessing calibration routine that ends with a bunch of calibrated color images--no alignment yet!. Then generate separate RGB images for every frame (there is a BatchChannelExtraction script).
align the R, G, and B channels separately, and make separate integrated (stacked) R, G, and B images. Then align those three and use the LRGB or other channel combine procedure, to get the color image. That should help, I hope.
Good Luck, Alex W.