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This is new since upgrade to 11.10, now when I click the system menus for notification icons, logged in user, etc on the top right, they don't stay open, they just close immediately.

Application menus on the top right do stay open correctly once clicked.

This is pretty inconsistent an awful, so how do I fix it? :)

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I've also encountered this problems. I have two screens, on the rightmost screen it works as expected (stays open), while on the left screen it doesn't – elzapp Oct 25 '11 at 19:24
Good catch, I'm seeing the same thing. Must be a multi-monitor bug. Seems like they didn't really test Unity in multi-monitor configurations much. – unit3 Oct 25 '11 at 19:52
up vote 2 down vote accepted

This has been addressed in an update to Unity:

The update has been pushed to oneiric-updates.

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