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Hey Dunk,
I suspect you probably know more on this topic than I do, but here goes...
How confident are you about your laser's collimation? Even if you're confident about that, does it always register the same in your focuser? I find that mine is a poor fit for my focuser and so it's basically useless for collimation. Good for doing things like tracking down collimation shift though...
Are you 100% sure that you have the autocollimator at the focal plane? Apparently you know you're "close enough" if the reflections in the AC are all the same size.
Based on the secondary shadow shifting either side of focus either your collimation is out as you've already guessed, or your focuser has slop... but re the fat-bottomed stars, are you sure your scope had reached thermal equilibrium?
Cheers,
Lee
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