Are you doing iterative 2 star alignments or doing the polar realign routine? The PA realign is absolutely useless, so don't use it - it told me I was 175° out once.
Also, don't do 3 star iterative alignments - I have found the errors are excessive. I do 2 star alignments on the SAME 2 stars in the SAME order each time - for instance I will use a-crux followed by Atria for the first. The second alignment I will do a-crux followed by Atria and so on until both MAZ and MEL are single digit seconds figures.
Also, best NOT to adjust az and el each time - I got much better results ONLY playing with azimuth until I got that sub-minute, THEN adjusting - finely - the elevation. And then rerunning the alignment.
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