I am using Unity. Today I upgraded some Metacity packages to the latest version with Synaptic Package Manager. After restarting the Window Buttons are gone, but the borders are still present.
See the screen shot:
I don't want to use Emerald.
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Quite likely what happened is that you have not upgraded a related package (such as the unity-window-decorator's required libs (metacity-common, libmetacity-private).
Wait a while, then check for updates manually again (