You would probably get a more straightforward answer if you explained your problem better.
Has it simply been since the new update or before?
Is it unread or read messaged that you cannot see? Or both?
These are some things people would probably like to know about your problem in order to help you with it.
The only problem with messaging I've ever had is If I haven't logged into SoM in a while. If a message or mulipte unread messages have disappeared then it could be because they timed out. If you leave a message unread for too long on SoM you can no longer read it anymore.