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its not always messages. it can blink for other apps. Facebook, weatherbug, ubertwitter... etc
look through ALL your apps.
If it wont turn off and you have no new messages just do a battery pull and that should fix the problem.
If you would have noticed, this person already does the battery pull and that is not a sufficient fix for the problem because they are always having to do it. There is a message coming into some app that they need to figure out where it is coming from.
its stays on when its charging. on the storm you can disable it on the storm 2 i haven't found a way to do so yet