try system wipe and reinstall, its working on mine after the new os. Also before the wipe try deleting the bluetooth and bridge profile on both the phone and playbook and re-syncing.
It works for me with the newest beta. Updraged from the latest 1.0.8. No wipe. I tap on the notification and the message pops up. The BBM notifications still hang once in a while.
If I don't need to respond to BBM tapping the reply box and just hitting the space bar will make it go away.