Is that DeepSky Stacker you are using? I had some similar registration issues as on the right until I changed some of the overlay parameters etc. I find I end up using 3 programmes to edit photos - DSS to stack, PS CS5 to do most corrections of colour, and MaxIM DL to tweak it a little.
I have SEVERE light pollution where I do most shoots - 3 mercury vapour street lights (2 that destroy my SW completely, almost ruling out the Sombrero and omega centauri), sports ground floodlights about 5 km away that seem to last till 11pm or so to the SE, and "city" haze lights to the east. I have NO view north except for a SMALL amount above my house roof!!! That limits my targets somewhat, but thankfully by the time Orion rises, the town lights are reduced significantly, the sports field is shut down and the heat has dissipated. So, I photograph m42 a LOT

TRIED on the Horsehead, but no matter how hard I try to fool myself, I can't see even a whisp of nebulosity around Alnitak
I limit my exposures to 2 minutes MAXIMUM on a good night, but usually 25 seconds at ISO800 or 13 seconds at ISO 1250. I end up with over 30 subs of Orion usually - should do even more - will try tonight to add to my collection already and do a MASSIVE stack session.
I should show my pre-process shots - green haze from tree reflections, orange glow from mercury vapour lamps or red wash from having to use ISO 5000 to grab a hint of NGC 253