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Notfications don't appear on my dual-head setup. When I unplug a monitor or set it to mirror, they show up. notify-send doesn't do anything. It's the same for the fglrx and open source drivers.

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So I figured it out. I have one big monitor on the left, and one smaller one on the bottom right. This leaves an empty spot in the virtual monitor on the top right. If I reposition it so the small monitor is in the top right, notify-osd works. Too bad, cause now the alignment (in the real world) is messed up. – Brian Feb 9 '12 at 5:46

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This question is a duplicate. This other post contains an screenshot to illustrate the issue, as well as a link to a patched package to address it:

Why are notifications appearing in the invisible black zone above my monitor?

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