"Thank you for contacting Ubisoft Technical Support. Unfortunately, the issue you are having is related to general gameplay hints and tips that is either covered in the manual, or is available via another source such as the Ubisoft forums (http://forums.ubi.com/).
I came here because I have the same problem. It's not just that I know fr sure I achieved these things, I've seen them red and "Achieved". That was before I finished the main story of the game. Now I have finished the story, then played the Christina and the Lost Da Vinci missions and now they are gone. Did the rest of you who have their achievements locked finished the main story? Maybe it's a bug or Ubisoft thinks we want a chance to re-achieve them if we want to replay the game again?