I'm sure the power to the Pi is always uninterrupted, but the mount's power supply acts weird sometimes, I'll investigate it further (though I'm rather sure that the power to the mount didn't go out, I was actively monitoring everything). I tried to replicate this issue today by using a camera and guide cam simulators (both internal and PHD2) and I couldn't encounter this issue. The only change was that I wasn't even touching my hand controller; it it possible that using a hand controller and Ekos at the same time could cause the mount to behave weirdly like I described in the first post?

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