I have to ask if you are using chrome, if you don't mind.
I have had similar issues with prioritizing rules and getting the game to update or save changes to player weights with chrome.
JDB helped with the rules issue (it's in bugs). However, the latter was not fixed by doing anything he mentioned there. I ended up deleting all of my previous weights (kinda bummer) and starting fresh. Thank goodness I had been writing them down when I realized there was an issue.