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I have been coming across this problem too. I didn't know if it was the Handcent app or stock messaging app. Do you use an app like Handcent? I'm not sure what the problem is. Handcent tells me that I have over a thousand messages in my phone but I only have about 50 at the most. I've been deleting them regularly because of getting this pop up message/warning. If it's Handcent then we should email them to see if they can fix the problem. If you use another app or the stock app then please let me know. If you are rooted and on a rom then it might be something overlooked by the developer.
All I know is I clear the cache and delete un-needed messages........