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Hi Paul,
I don't know your controller so this may be irrelevant but is the scope setup correctly in the software? I recently used an Argo Navis controller on a different scope and had very similar symptoms to yours. I thought the new scope was 10,000 step on both axis but the very old encoders were only 8500 steps in az (actually empirically measured at 8532). Goto accuracy was in the 5-30 degree range! I know in one has encoders and the other stepper motors but the principle is the same.
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