Does this still happen if you disable Unredirect Fullscreen WIndows? You
can do so by installing the compizconfig-settings-manager package then
going to System->Preferences->CompizConfig Settings Manager. The setting
is in the General Options.
** Changed in: compiz (Ubuntu)
Status: New => Incomplete
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Mouse sensibility changes while popup/notification while playing fullscreen 3D
Games
https://bugs.launchpad.net/bugs/420419
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