It happened to me too when I read the mails you get right after starting Chapter 2, I had already read them in a previous save but remembered that I missed a quest from CH1 so reloaded that, finished it, and then started Chapter 2 again, and then there was the new mail symbol but no messages in the unread mails section. What I did was go over to my read mails, and there they were already, so I just re-read them from there and it got fixed