Thanks for the explanation, that makes sense.
I've had my EQ6R-Pro carefully situated in my backyard for quite sometime and since I got such a good PA I've been very very cautious to not disturb it. On those nights that were clear enough I'd first check the PA and it has been holding very well. Then I did an update on Stellarmate and everything (seemingly) went nuts.
Lat night, after seeing your message, I disabled meridian flip and voila: I could use the mount again. Did the PA check and it was off by a lot, just a shade over 3 degrees in Altitude.
I did not do the thorough analysis you did and thus have no idea if that was just coincidence or not (instead just corrected the PA and happily continued).

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