I suspect your polar alignment is the problem. Using the polar scope without a follow up with a drift alignment will give goto errors.
That is why multi star alignment is used as it can provide correction for polar and cone errors.
The first check you should do after the two star alignment is to do a slew to a new star a long way off (don't centre it or move the slew buttons) and then back to the original. If the original is still in the same place polar alignment is the problem. If it is not the problem is mechanical and will need to be corrected first. This sort of problem can be poor balance, overload. excessive backlash or even a faulty mount.
Meridian flip is also a possible source of errors especially if it occurs during the selection of two alignment stars.
Barry
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