"Primary" means a post that is primary in the thread. I suppose it would have been clearer to say "reply" instead of "non-priamry".

Your average karma gets hit because primaries tend to get much higher karma than replies-to-replies-to-replies that few people read. My primaries probably average 15-20, but I have a lot of 1-pointers in nested discussions that I think are better than the 50+ primaries.