I frequently use a DSI for color and a DSI Pro for luminance and this method works quite well. I've found that Autocontrast on the DSI tends to set the black point a tad too high which could cause some of what you're seeing. Try turning Autocontrast off and lowering the balck point 1,000-2,000 counts. I also save all of my uncombined images as FITS3P so I can re-stack and re-process them using Envisage offline.
-John