Steve is right. Use auto refresh, but wait for the 2nd refresh to ensure you're seeing the latest results of your alignment. Or, turn off auto refresh and refresh manually after making adjustments. Sometimes polar alignment takes me 15 or 20 minutes, but I aim to get it down to within 50" on each axis.
Another tip I learned: Do your first alignment with the Azimuth and Altitude levers unlocked. Then do another one but this time tighten your Azimuth an Altitude levers about half-way, so you feel a bit of tension when making adjustments. Keep tightening your Azimuth and Altitude locks a little more each time and when you've got the PA to where you want it then tighten the locks completely. This takes more time, but your autoguiding will be that much better. Last night I imaged two nebula (NGC1893 & IC 405) and my guiding was as low as .27" (DEC) and .35" (RA). Here are the RESULTS (113 subs at 120" each).