I haven't been on here in forever, work is kicking my ass. Anyway I've been working on a custom theme but have had this problem. So the icons if they aren't system icons show up with a black rounded sqaure icon behind them. However now I'm having a problem where some icons show up with a rounded icon overlayed over the actual icon while others are fine. I've searched through the ones that it happens to but I can't find out what determines which ones have this overlay and which ones don't. You can see what I mean in the screenshot below I have underlined two icons you'll see the difference between them.