It's all done in J2000, however if "Telescope needs Local Topocentric Coordinates" is ON (Telescope tab) all coordinated in and out of the telescope are precessed to and from "Jnow" (which is actually a misnomer, the proper name is Local Topocentric or just Topocentric) by virtue of the USNO NOVAS Positional Astronomy algorithms. It appears to me that the problem you are seeing is the mount's initial positional accuracy is off. There is a "homing" function as I mentioned by looking at the docs. I don't know why it powers up with an error. Maybe it requires parking before shutdown? What happens if you don't shut it down? ACP leaves the tracking turned off so this is safe.

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