I have a new idea about what might be causing the skewed shots - the camera is on a bit of an angle when afocally held to the eyepiece by my bracket. I assume this contributes to it, as well as skews the colours? I was considering taking the tripod out last night to push the bracket up a little bit to see if it helped, but the jetstream stopped me going out.
As for vitrualdub/ppmcentre, seeing as tomorrow is a holiday, I might give them a try. I've never used virtualdub, but I've given ppmcentre a quick go. Tomorrow looks like a processing day =) (Plus, lets hope there are some gaps in the clouds later tonight before midnight to sneak in a quick last image or two

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