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Hi Graham
if the CCD looks fairly well centered when you look into the front of the camera, then it should be lined up OK.
One possibility is that you might have light leaking into the system somewhere - the Ha image should be very much darker than the others, but it doesn't look like it is. could light be getting into the filter wheel or the camera?
Running a sensitive camera in ambient light with no optics may well overload the CCD and mask what is going on. Do you have any of your night-time sky or lightbox flats that you could post? A dark could also be useful - these symptoms could possibly be caused by Peltier cooler issues.
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