i have ubuntu 11.04, and I recently got an apple monitor for mac from my uncle to replace my old thick monitor. It works fine, but suddenly when I open blender i can see right through it to the desktop. It doesn't do this for any other application, nor did it do it for my old monitor.
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Could you pose you're system specs from the help menu?, its useful to know what drivers cause this.
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Tested in Ubuntu 32bit with GeForce 6800 XT proprietary drivers, didn't have this problem.
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It didn't let me attach the file, so here is the link: http://www.pasteall.org/25643/text
Your computer is different from mine so it would work for you
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Such behavior is likely caused by a bug in either the graphics driver or the window manager, it seems unlikely the monitor could influence this. I've seen this behavior a few times with an NVidia GTX 460 using official drivers, but it's quite rare and I have not found a way to redo it.
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Yeah I had to get a new video card for the monitor to plug in... Hadn't even thought of that it's probably the new card not the monitor. So we can work from there.
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Did you try to disable all desktop effects and run blender without them? If it's still fail for you, disable desktop effects and try running blender-softwaregl script.
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I already do use blendergl because of the last glitch... And disabling desktop effects doesn't work because I can still see right through to my icons.