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I just installed vncserver/vncviewer, ran vncserver :1 on my remote machine, used ssvnc to connect to it from my local machine. It works fine, I'm happy, but I would be even happier if I could find the windows that are open on the remote desktop ! I wish I had enough reputation to post images, instead I will post fake pictures and hope my point gets across. See "Figures" below

I am running Kubuntu on the remote machine.

REMOTE DESKTOP SEEN FROM LOCAL MACHINE

*******************************************
*                                         *
*                                         *
*                                         *
*                                         *
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REMOTE DESKTOP SEEN FROM REMOTE MACHINE

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*            APPLICATION WINDOW 1         *
*                                         *
*                                         *
*            APPLICATION WINDOW 2         *
*******************************************
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You do create a new display with vncserver :1. Are you sure you are looking at the same screen both times? Can you provide the vncviewer commands you used for each connection? And from where did thos application get started? –  Anthon Jun 7 '13 at 17:57
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