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I would ask a similar question to what Martin did, what are your RA and DEC RMS figures? If the RA is great and the Dec just so-so you might get a reasonable looking overall RMS but elongated stars in Dec.
That said, can you pop up a pic of what a full frame sub looks like? That might give a hint as to where to start, guiding/tracking issues will show one sort of characteristic error, polar alignment another and backfocus/tilt a different one again.
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