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Lee - I had the same occasional issues in the past. The new version of SGP has an improved algorithm for focusing and it works for me every time, and I only shoot nebulae in narrowband :-)
Brett- if the chip is tilted, even slightly so, then checking with a mask on a bright star that is on axis may give a slightly different focus point than SGP that averages HDR for many stars across the chip and thus finds optimal position that will/should yield on average the sharpest stars in the entire image.
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