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It could also be flexure between the guide and main OTAs, or the camera isn't square, or the guidescope isn't square.
My understanding is that you should balance the setup first (with camera attached), in both axis. Then you should do a rough polar align, and then a drift align. You shouldn't need to change the balance for polar alignment, it should be simply adjusting latitude and azimuth (I think that's the right term for what I mean).
Dave
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