Same issue for me: mouse cursor does move, but no click nor focus under
some unknown circumstances. I also use two displays with xinerama
connected to the same video card. Before upgrading to 8.10 I was using
7.10 and 8.04 without any issue.

** Attachment added: "xorg.conf"
   http://launchpadlibrarian.net/19907836/xorg.conf

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Mouse focus and clicking stops working
https://bugs.launchpad.net/bugs/290406
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