I've had my Conky configuration properly working in Ubuntu 12.04 for sometime. After a recent update and reboot Conky is showing up on the Unity Launcher as an entry when it is running. It's not locked to the Launcher. When Conky is killed it goes away. Nothing has changed in my Conky configuration and otherwise it is working properly. I'm just looking for it to be blacklisted from the Launcher while running.
In the screenshot you can see the Conky entry third from the bottom.