[House]

Like what apristel said, it might be something that you might have installed. I've been running 6.5 and 6.5.1 on my TP2 and I haven't noticed any phantom message boxes at all (I got phone to check three mail accounts every 2 hours). Try disabling the message on screen popup, perhaps that's what's causing it? You could also try hard resetting and pulling out the battery for a minute or two after hard resetting.

Also, did this ever happen to you in 6.1?