One thing you could try is focusing on a different patch of sky, say, just a star field, and then slew to your main object once you're happy with the focus?
Saying that though, the software is intended to discount galaxy cores etc from the FWHM measurement. If you have some raw images of the FWHM causing you problems, you can always send them to chrisg@atik-cameras.com to take a look at.
Jo