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I just had a new desktop constructed and installed ubuntu 12.10 which was successful for the most part but every time I open up some applications like thunderbird I get automatically logged out and all my windows are closed. System error messages also come up from time to time.

Also I'm not sure if this helps but if I select the "Use system title bar and borders" in chromium I will also get logged out and from that point won't be able to use it without getting logged out in the future. If I click on particular links as well.

If anyone has any tips on how I can isolate and fix the problem I would greatly appreciate it.

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I was experiencing the same problem. What seems to have solved the problem for me, though I don't know how, is installing an NVIDIA binary driver. If you have an NVIDA graphics card, this might work for you too.

But beware, there appears to be a bug in the NVIDIA driver package (see e.g. here: Desktop does not show when I installed nvidia drivers!). You need to first run:

sudo apt-get install linux-headers-generic

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