After using the polar alignment utility, I usually do another two-star align ( or three-star if you prefer ). This will give me the new error amount. It will be lower than before.
Then I go back to utilities/polar align again, choose a star to use ( usually the same as the last polar align ) and follow the controllers instructions.
Once this is completed, I do another two-star align and see what the error is. By now it's usually very low error.
If it's not, or it gets worse, I use the utilities/curse&swear function.
Hope this helps.