The measurements are being made differently. PHD2 estimates polar alignment error based on the rate of drift in Declination. That's an objective measurement but the cause of the drift could be something other than simple polar alignment error. So if you have recent to doubt that it's due to polar alignment, you will need to find another cause: flexure in the mount payload, substantial imbalance of the OTA in Dec, hanging cables, a loose clutch, etc. If you look at the unguided Dec behavior for extended times on each side of the meridian, that may point you in the right direction. Since you didn't upload any data, that's about all I can tell you.
Regards,
Bruce