The second one is from a previously installed MOd in that subSystem forum tempalte. When we firts started modding that theme, we noticed it was FULL of hacks. We obviously missed that one.
The solution may be as simple as replacing the corresponding tpl file with the one from the original subSilver from the origianl phpBB ported Forums. We'll look into it.
As for the Private messages. I have noticed some other users on other sites reporting Private message count was wrong and always kept telling them they have new messages.

That may have a fix for it already...

mikem