Chance is you are not using the latest stable release. Quick fix: deactivate the tickbox "Meridian Flip - Flip if HA>" in the mount tab. In the latest stable release this problem (for my setup a problem in the EQModMount driver) has been fixed. We'll in theory according to the displays since I had no clear night's for 3 month to confirm.
Search for Polar Alignment Problem in this forum for more details.