Hmm, could it be that you have empty checkboxes selected on your menucards (in the admin)? I do asume you have checked at least some checkboxes since you have two seperate menucards 😉 I remember that some users imported the dummy content, then deleted everything, which caused the menucards to remember deleted categories. This caused the menucard to show everything in one column. Play around with unchecking all categories on your menucard, and then selecting them again. This may sound strange but it might work since this is how the others fixed it as well.
Hope this helps 🙂