I have the same problem and its consistent. I run Lotus Notes 8.01 under
Wine (1.0.1-0Ubuntu2) and it works fine if I don't switch desktops. My
setup is Ubuntu Intrepid (with all current updates), ATI FGLRX graphics
driver, Compiz and AWN Manager. I have a terminal running in the
background so I know the application is still running but the Lotus
Notes icon has disappeared from AWN and the Lotus Notes application has
disappeared from the desktop. I usually have to kill the processes and
restart the application. Any ideas?

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Fullscreen wine applications disapear from window list on workspace switch
https://bugs.launchpad.net/bugs/156542
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