Or that they have some other reason to have not learned as much (say, worse primary schools? differing cultural values?).

It is very well known that affirmative action tends to take the form of lowering standards for the groups being favored. If this is in fact true, running into a non-biased filter would tend to undo some of its effects. As noted towards the end of the post you're calling offensive (We also need to remember that many universities have quotas for minorities and give extra points on the SAT for just checking a box.). If this is not true... a weed-out class would not be observed to change the class demographics.