meineko Next time, I will remember to uncheck RAW in the save options.
Actually, you do want to capture as raw (i.e., every pixel from the sensor remains unaltered).
This way, the stacking program has a chance to treat the red Bayer pixels differently from blue and green Bayer pixels.
As you know, unless a target is straight up at Zenith, it will go through some atmospheric refraction.
Not just refraction, but different wavelengths of light will refract at a different angle; this is called atmospheric dispersion. Dispersion is what causes a rainbow to form bands of different colors. Similarly, this dispersion will cause the red component of a planet to arrive at a different angle as the blue component, for example. I.e., the R, G and B Bayer cells of the sensor are displaced from one another.
Good processors will realign it properly for you -- that is why you do not really need to use the automatic dispersion correctors when doing planetary astrophotography, like this device that is used visually:
(There are cheaper ADC that are manual instead of electronic, but hey, this is the 21st century.)
Anyhow, if you deBayer the image before taking care of atmosheric dispersion or let the ADC do it for you, and if the deBayer algorithm combines the components (this is done to extract more "resolution" from a color camera), then the stacking program cannot avoid smearing the different components. I.e., the resultant color image would not be as sharp and vibrant (saturated) as possible.
Basically, you should capture and save the "movie" as RAW AVI format, but tell the stacking program that the images are taken from a Bayer color camera (and using RGB Drizzle usually helps further).