it just means that that icon is hidden. you want to highlight that icon and hold down the alt/half moon key and click in on the trackwheel. once you do that it will give you options to show all, hide, or move the application/icon. if you highlight the messages icon, hold down on the key, and click in the wheel you will have a checkmark beside hide and show all. just click on hide to uncheck it, and it will be as good as new
