I haven't noticed any numbering inconsistancies with the system. My best guess is that it's confusing due to the fact that the number is only correct on your most recent post. The number is generated when you create the post but is not updated in all your previous posts when you write a new post.
So if you look at a message you posted 5 messages ago, the number will be 5 less than the number under your most recent post.
I think it may go back and update all your other posts with your current message count when I reindex a forum, but I haven't done that in a while.