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Could be backlash in the Dec and/or RA - is it possible to increase the 2500 ms max pulse?
Might be also worth trying to use a small box around the star for guiding - I used to have issues with sudden movements that were caused by some random interference pattern in guide subs, which disappeared when I started using a small box around the star - I guess less traffic/data flows via USB.
But I'm guessing your particular issue is caused by excessive backlash in at least one of the axes.
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