Update - After 2 weeks of using it on iOS8.3, I am disappointed to say that atleast on my iphone, this problem has become more wierd.
1. Now the the unread messages stay in notification centre for much longer time than before, but it takes around 2 days or some trigger to make them disappear from the list. I am still not able to find out what that "trigger" is.
2. Also, now if you just restart ur phone Or the phone battery finishes, then when you recharge & start it up back again, all the unread messages simply disappear from the notification centre.
So the issue has gone from bad to worse. Why cant Apple get their native Message app fixed ?
If any has found a new solution ( have tried almost everything that exists on internet/forums) , please let me know. It will be helpful
Regards