I sometimes don't receive messages BUT I get the ringtone, and flashing light indicating I have received the message. I have nothing in either the stock, nor Go SMS app. I had the same issue with Handcent which is why I'm using Go SMS. It is quite frustrating when I'm carrying on a conversation via text and get the ringtone, but nothing on the apps. This didn't start immediately after going back stock/rooted.

Is anyone else having this problem?

I'm rooted but running stock (I had to find the stock OS on line).