Thanks David,
Fingers crossed, I think the Bayer matrix FITS settings is the key here, I am stacking some now to see if its the case, hope so! It certainly makes sense considering my RAW stacks look monochrome more than colour....hmmmm.......
I will keep you informed of the results....I'm doing M104 at the moment, but I think I might just stack M20 here and show the unprocessed stack result for comparison if this fixes it....
Thanks for the nudge in the right direction (stay tuned)
Cheers
Chris