I think I am in the same boat. I am using ACF Pro 5.2.0 and WordPress 4.1.1
I have no rules set up on the regular ‘post’ post_type at all, and have checked (and checked again) all other rules, and none apply to posts, yet when I click on a category to assign my post to, the category meta box disappears completely. Re-showing it from the Screen Options panel does work, but it disappears again after selecting another category.
