Ok I have not been on standard TP2 sprint WM 6.1 rom in a while (this was an issue only 6.1 rom), so I have not dealt with this issue in a some time. If you want to get rid of it all together flash to a new rom, thier great (Mighty Mike, NRGz28, Deck sss rom, etc) here is a video link if you have any questions.
http://video.najoomi.com/list/rhodiu...e/start-1.html
How to flash a CDMA TP2
But if you want to find a fix for your issue, google "phantom messaging on Touch pro 2" from the search, I remeber back before we started unlocking and flashing our devices this was an issue. Manny people nick named it the phantom messaging issue. becuase it gave the appearance you have a new message even if you alread checked it. Hope this helps.