Alan,
Concerning the PM popup problem, does your unread PM count increase upon a warning? I think you may see that it won't. Those of us who have the PM popup option turned off will never see an indication of a new PM. Try turning off your PM popup option: AdminCP -> vBulletin Options -> Private Messaging Options -> Instant Messaging Support - Check for New Private Messages.
Maybe this will help you solve the problem.
Thanks!
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