So, You're saying that the launcher is now Nova? and not the default launcher? That could be why you're not getting the indicator on the text message icon. If this is what you're talking about, goto settings>General>Application Manager: Then scroll over to "ALL". Then find Nova Launcher, select it, then scroll down to "clear defaults"....now hit the home button and this should bring you to an option to select "touchwiz home", select that, then you should be back at your default touch wiz launcher. I believe this should correct your message issue as well.