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Were you using the same alignment stars as the HC? I think (but don't quote me on this) the algorithm used is different between EQMOD and the Synscan controller. Assuming they are different, one would expect a slightly different result? I know I wouldn't expect that but it could be possible. When I was using EQMOD a couple of years ago, I found one star alignment enough when the mount was properly aligned.
If you are a member of the EQMOD yahoogroups, have you put the question forward to them?
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