The tools aren't actually meant to disappear. They're buttons so if you click them once, a bar will disappear, but if you click them again, the bar will reappear. I did it that way so that when a team gets a "steal one" slide, the team they steal something from will have a bar added back.
I suppose it'd be simple enough a fix if you want to make it so they disappear after one use, though. Do whatever you need to do to make it work best for you!
EDIT: If you mean that the bars are reappearing when they aren't supposed to, then that's probably a powerpoint compatibility issue. Sadly, some animations/functions don't work consistently between versions of powerpoint. That's why I always recommend taking a newly downloaded PPT for a test drive on the computer you'll be presenting it with before actually using it in class.