The problem is not the design of the icons. Yappari provides a 16x16 icon for the status area. If you create another icon, still providing a 16x16 alternative, the problems will probably persist. I guess that the packages of the Humanity theme/humanity icons need fixing. It should be certainly done in the packaging of these apps. But I'm not into theming, so I don't know how to do it. But if you compare the built-in hicolor theme package with the humanity-icons package you may find the cause.