Graham,
I am very new to this but I use DSS. DSS does accept canon RAW files but it may modify them. I use Startools for processing, and it likes the stacked file to be as unprocessed as possible.
So I use dcraw to convert RAW to TIFF as described here:
http://www.startools.org/forum/viewt...67&hilit=dcraw
Startools likes the output file to be saved as FITS 32bit integer.
I have turned off any processing in DSS - can't remember it all off the top of me head.
Ivo who wrote Startools told me all of this. It seems to have improved my images.