I had been having what seems the same problem (things like tapping the app screen, but the screen freezing for a few seconds and then going into Edit Mode with the red crosses over the apps, key popups freezing, key clicks not registering and then hearing them all at once) in the end I took the plunge and just reflashed my N9. Unfortunately I wasn't able to put in Open Mode while I was at it, but at least now it seems to be solved. I hope just doing a system reset is enough for you. However, I seriously suspect of MeeCast. It's the only app I haven't reinstalled but before the reflash it always shown "no data" or a red X over it on the Event Feed.