I think this is a gnome problem as well, not just nvidia. I have this
same problem using an X config with an Intel display on :0.0 and a
sisusb on display :0.1. This configuration worked fine in Intrepid, but
since upgrading to Jaunty, gnome applications no longer open from the
launcher on the :0.1 display. (However, firefox and some others will
open fine on :0.1)

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Separate X-screen, apps launched from 2nd screen appear on first screen
https://bugs.launchpad.net/bugs/339783
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