Whenever I start a sequence, SGP focuses first then does a platesolve then focuses again before starting to capture. I did have platesolve use a certain filter so perhaps that’s it? ie it changes filter to the one for platesolving then platesolves then changes to imaging filter and focuses again? Seem s bit over the top. (If I’m imaging with say an Ha filter I had a CLS LP filter as standard for platesolving - perhaps unticking use a specific filter would solve it?) 
Looks to me like you are asking it to focus twice … once before the sequence starts, and again after the plate solve and centering.
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Earlier versions of SGP would do all the centering before focus. That could cause issues if the image was not focused in the first place. In response to customer suggestions, AF was done prior to plate solving.
If I have a filter wheel on a camera, I usefully spend a few hours working out the focus shift with each filter (one time only). I then populate those figures into the filter wheel tab and then I do not need the option ‘auto focus on filter change’, rather the adjust focus with filter on the main focus tab in the control panel. It makes things much faster and also allow one to focus with a clear filter and use shorter exposures.
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