What would cause the cylinder not to line up with the hammer? Notice the nice crisp edges on the cylinder stops, so the bolt is hitting the slot perfectly, but it is just off to one side on the hammer. My Walker does the same thing, but doesn't hit the side of the hammer slot, it's just really close.
http://i613.photobucket.com/albums/tt214/shutupandjump/colt-cylinder.jpg
http://i613.photobucket.com/albums/tt214/shutupandjump/colt-cylinder.jpg