The initial altitude number it wants you to set it at before you start polar alignment is based on the original level calibration. If, for example, it always tells you you're need to dial 2 degrees down to match latitude, and then you do the polar align and it wants 2 degrees back up, then it means your level calibration itself is off by 2 degrees. I saw this at some point after a firmware update, and simply redid my level calibration until it stopped doing that. If that doesn't fix it then you might have to fake it out by adding some thin shims during level calibration so that you're actually calibrating it 2 degrees off physically level until they match.
Also.. (like many others) ignore the Refresh Deviation button. It always gives me wildly wrong polar align values. If it needs to be done done again, then go back out to the advanced menu and come back into EQ menu.
