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I have multi-monitor setup where one (separate) is set above another (notebook). Notebook is set as main monitor, this is where launcher is. There are a couple side effects:

  1. When I open a new app, ex. nautilus, it appears on top screen while the mouse and launcher is on the bottom (notebook)

  2. When I unplug top monitor, some windows (ex. skype, zim, console) appear to be below notebook and thus invisible. I can only access them by focusing using alt-tab and then ctrl-space + Move window

I use Unity with Ubuntu 12.04, intel sandy bridge built-in video. Any tips? Is it known bug?

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I know that the first problem is caused by ubuntu wanting to open the app in the middle of the screen. Likely, your separate screen is a little bigger, so instead of opening the app window in-between two screens, it opens it on the one closest to the middle. I'm not sure how you would change that. –  Serendipity Jul 3 '12 at 19:30
    
Have you tried tinkering with the monitor settings? How about graphics card drivers? –  Seth Feb 20 at 17:18
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