Matt, I still think that those apps are wrong. Here's two screenshots from my computer. I submitted a bug to fix the keyboard layout text. The universal access indicator (you only get this if you go to System Settings>Universal Access>Typing>Turn on accessibility features from the keyboard) is broken in so many ways that it should just be disabled for now; at least it's a bit hidden.
Even though Tomboy doesn't really follow the right style, it's still easy to tell that it's Tomboy Preferences. Therefore, it's a bug in the other apps you're using to not use the indicator API correctly.