I've searched the forum for posts about this topic and they were either really old, or they were never answered. I have 4 sites in co-op, 2 are giving me positive weight, 2 are giving me negative weight. All 4 are green. All 4 use the exact same code, as they are ASP includes from the same shared source. Ideas? Maybe a clue or some help?
OK, so with no expectation of an answer in sight, I decided to do some experimentation. I have a Google API key so I can check and recheck weight/validation as much as I want. I tested moving the links to different places in the site's HTML. I removed the links, failed validation, re-added the links, revalidated. None of this worked. This was on top of waiting a number of days to see if things "reset" themselves on their own. Then I turned off rel=nofollow, and voila, positive weight. I think there is either a new bug in the penalty calculations for rel=nofollow or the code Sean fixed years ago regressed via other updates. It also seems that only certain scenarios cause this to happen... I can give more insight into the scenarios if anyone is interested.
That's great you've managed to get that to work. Someone I know has been having that problem for three years...