If you have installed Ubuntu Natty Narwhal Alpha 1, you will notice the new Unity interface and hence no Gnome Panel(s) anymore. Since “Run Application” dialog is a part of gnome-panel, it is not possible to enable the same “Run Application” dialog. If you wish, you can achieve that by running the gnome-panel, but this is not the recommended course of action if you wish to keep running unity.
So, the other way to make it work is to use third party run dialogs from repositories. One of the best run dialog is gmrun. It is available in Ubuntu universe repositories. Open up the terminal (by pressing Ctrl+Alt+T) and type in the following to launch Synaptic Package Manager: Continue Reading

UPDATE: I figured the problem was due to messed up compiz settings. Disabling and enabling compiz (Right Click on Desktop>Change Desktop Background>Visual Effects None and then again to Normal or Extra) fixed it.
The older post follows.

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If you have conky installed, then by default when you click on Show Desktop icon on your panel, conky also gets minimized. You can bring it back by clicking it again, but that does not work if you open another window or selectively maximize/restore a window(s). Also, when you click on the Desktop after activating scale, then conky is lost. In both of these cases, the conky process keeps running, however it cannot be brought back. You must terminate it and run conky again.

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