I am in the process of learning to use Kstars/Ekos and was testing autofocus yesterday when I noticed the very behaviour you describe. Auto select star checkbox results in a star being selected in the upper left corner. I am using a rasberry pi 3b+ with the stellarmate os ( downloaded 20190404 - so quite new 
My focuser is pegasus astro - dmfc driver
Are there any specific news or settings related to this issue, available?
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