Try downloading a different messaging app. Set it up then clear data from the stock app. Then turn off notifications in the stock app and turn them on in the new app. Have someone send you a text and see if you get the proper number in the new app and not the old. Then read that message in the new app to see if the unread count goes away in the new app. Then check the stock app again.
If that doesn't work, hide the stock app icon for a few days and try using the new app. It will probably eventually go away in the stock app but keep checking. Seems like I had something like this a while back and I tinkered with the the new app/old app gymnastics as above until it went away. If nothing else, it will be out of sight and you'll have a better 3rd party app. I'm using Go but Handcent is good too.
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