Im glad it gave you a good heads up, do remember though a 3 star alignment will adjust for Cone error.
Cone error comes from the telescope not being parallel to the mount head.
what the proceedure you have done, does set your Home position, that is having everything at zero when you start the mount as when you start the mount it assumes everything is at the home position (zero) before heading off.
try it sometime put the scope on a obvious tilt in the RA, turn the mount on, move it with the paddle, then in the synscan hand paddle select Park Scope, the scope will move back to where you had it initially.
Once you have levelled the tripod out and then done this proceedure for home position use a permanent marker to mark the spot as the rings i have found to move around on you. be careful
