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I had similar issues with my Sitech Controller and Gemini Motors, turned out i needed to add some pullup resitors to the Encoders. At slow slew speeds the motors would turn without issue, but when slewed at high speed the motors would stall. Essentially the encoders were lossing position.
The newer sitech controller comes with the pullup resitors but the old one did not. From your intial descriptuon it seems the issue is on the RA output port of your Gemini. Might it be possible that similar pullup resistors on this output are faulty.
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