Gday Chris
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I have operated this mount successfully for a couple of years and the normal 'Home' position has always been due south, scope pointing at the SCP,
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Thats 100% correct
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but there are 2 "mechanical" ways to achieve that if you are "manually" putting the scope in that position :-)
There is only one way if the mount uses its internal sensors.
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It seems to me as if when finding home position, the mount chose a location closest to where the scope was pointing at the time
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Nope, it chose a spot where its internal home detection system said the internal sensor changed state.
Simplest solution is to do an auto home via the handbox
If scope is pointing wrong way ( as yours is ), undo DEC dovetail clamps and rotate scope 180deg and refit.
All should be well after that.
The encoders are reset on every boot, ie they have no real idea where they are until you align or home, but the home sensors are mechanically fixed.
( Also note the "mechanical" home sensors arent fitted very accurately,
so even after using the "Find home" functions, you could still be off by several degrees )
Andrew