I don't know what to tell you guys. I just used
http://addon.bool.no/ to generate an addon, and it's identical to the addon I already made manually ages ago. I even loaded it in-game and it works exactly the same. For example, when I look at the achievement UI on a character that has not done any of the Noblegarden achievements, without the addon, they're all shown as completed (because other characters on my account have done them); with the addon, they're shown as incomplete. Same goes for the kill-related tooltip lines from Overachiever; I'm still seeing them on critters -- my level 1 auction alt has not killed any critters, gets a green "already killed" line without the addon, red "need to kill" line with it. I didn't go find a rare spawn to check, but I assume it would also show the same thing.
You guys must be doing something wrong, but I have no idea what could possibly go wrong with a simple copy-paste... I've attached the working ZIP file in any case. If it still doesn't work, then I guess you have gremlins, and there's not really anything else I can do to help you.