Is you're "Use Status Bar" option in IntelliScreens settings chekrd to "On"? That may also be it.
If that's not, there's a very interesting error that I've found.
I'd you get an incoming call while your phone is locked, and you ignore it... Then UNLOCK your phone and go about your business, if you get a new voicemail, intelliscreen will pop up the alerts over whatever you're doing. Going to your home screen doesn't help. Only locking and then unlocking your screen will make it go away.