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Thanks guys.
RickS, I know field rotation will be an issue, however if the alignment is pointed at least vaguely in the right direction it won't be anywhere near enough to make any difference for subs under less than 5 mins. Not an issue I'm worried about.
Billdan, your answer makes a lot of sense... although I can't help but feel that it's a fairly large failing on the part of the mount if it can't make small enough adjustments to deal with such things. An NEQ6 costs a fairly respectable amount but it is, when you get down to it, a fairly simple mechanical device. Mildly surprised & slightly disappointed that it can't make subtle adjustments without slewing all over the place. RA affecting DEC should just not be an issue if the adjustments are small. I know there are a lot of variables, like wind / vibration / backlash etc, but I would have expected a precision instrument being instructed by a high-speed processor (such as those found in literally any laptop made in the past 10 years) to be more than up to the task if the mount was designed better. I dunno. I'm the furthest thing from a mechanical engineer so I'm not at all qualified to assert such a thing. Just disappointed, because in principle it seems like a pretty easy thing to program: if the star moves, counter it.
However, the bigger issue for me personally has been answered; my mount SHOULD be able to track a star all night regardless of alignment, whatever other backlash / adjustment issues might affect the subs, yet it keeps losing the guide star. Not every time, but often enough. So that's not just a matter of slightly bad alignment? Because I didn't think it could be. I've suspected for a while that there's something fundamentally broken about my guiding setup, and this kind of suggests strongly I was right.
Sigh...
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