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Which handset software version are you using? I use a Synscan with the GPD2 and NEQ6 and I do an iterative polar realign too (SO much easier and quicker than a drift alignment and can get it sub minute in around 4 iterations on average in both axes) and have NEVER seen it suggest alternate stars UNLESS I change from a 2 star align to a 3 star alignment.
To be honest, I always found the 3 star alignment poor compared to the 2 star with a subsequent PAE subsequent align on another star in the other horizon (usually not much off anyway, and now the error is reduced even more). In total, I do a 2 star align with whatever iterations it takes to get sub-minute on both, then do refinements with PAE on at least 4 more stars, and I ALWAYS have the resulting AP target almost smack bang centre of chip every time.
If you are Synscan 3.35, can I suggest reversion to 3.28 Beta 15 or 3.27
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