If you're using the more recent Synscan versions, it's the error in polar alignment IIRC.
After the 2 or 3 star align, you can go into Align->Polar and it will guide you through steps to make your polar alignment better. So long as your polar alignment isn't too way off already, just the 2 or 3 star alignment should be good enough for visual, but I've been using the polar alignment feature for the last few sessions and it gives spot on gotos all over the sky
or maybe I got lucky
