My gut feeling is that the judges knew that Joubert had not done enough technically and therefore to keep him in second they had to bolster his PCS.
Wait, what? Are you implying he should not have been second?! He had 6 points technically over Johnny Weir, who ended up third, so a couple of points off Joubert's PCS would not have made a difference. And as much as I love Johnny, there is no way his performance was better than Brian's. Brian fought with passion and confidence, and Johnny had a "Dear God, please let this end" expression on his face throughout his FS. I am proud of him for pulling through, but he was kind of lucky to get third. There is no way Brian should have been below him, sorry.