OS X 10.11 introduced a new feature for having the menu bar automatically show and hide. When this feature is enabled while creating a QSystemTrayIcon, the resultant icon in the menu bar will be blank and invisible.

Looking into the source code, I think the problem is in qcocoasystemtrayicon.mm. In this circumstance the reported height of the menu bar using [[[NSApplication sharedApplication] mainMenu] menuBarHeight] will be 0 pixels, causing the icon to be resized down into oblivion.