The bug happens when you start up the phone and you don't open the Messages menu right away. If you leave the phone after booting and not open the Messages menu, the messages stored on the phone will not be read at all and new messages wont show up. You must go to the Messages menu so the phone will open your messages and receive new ones.
I think the bug only appears to those who store a lot of messages in the phone memory and to those who doesn't turn off the phone properly causing a corrupt message database that must be repaired by the phone.
Hope arctu can post his fix. So that the people experiencing the bug can at least repair the problem while waiting for the finished firmware.