I have been having this problem as well since the newest Android upgrade on Aug 2nd (G930vvrs4crg2) and June 11 (g930vvru4cre5). I run the latest version of Message+ (Version 6.6.7). Sometimes it works correctly, other times it does not. It will still pop up over the status bar, sometimes it will make an alert sound,  sometimes it won't. Sometimes it let's through my favorite people, other times it doesn't.