It seems to have resolved a number of issues in the current production version of FF26. The check boxes I tried behave, the addon bar no longer automatically pops up every time I open the browser, and the badge on the addon bar is removable.
Wishlist: The ability to permanently relocate the Foxy badge, now alllllll the way over in the corner, to it's old location in the middle of my toolbar (and in my field of vision).