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I'm having troubles possibly because of two graphics cards. I want to do CUDA development, so I installed an cuda-compatible NVidia GeForce 8400 card. The 8400 also took over the task of driving my monitor. To use cuda-gdb, the card has to be fully devoted to the debugged task. And the embedded graphics processor on my ancient motherboard won't function if there is a graphics card installed. So I needed something to drive my monitor.
Also I only have one PCI-E slot, which is used by the 8400. So to run my monitor I picked up an GeForce 6200 PCI card.
I was getting strange results. The (lightdm?) login screen looked fine but the gnome desktop showed up at the wrong resolution and I only saw a portion of the desktop. So I decided to replace the driver. I went to Nvidia and downloaded NVIDIA-Linux-x86-304.64.run and did the install process. (Previously I'd been using ...304.43.run, I think.
Now the login looks fine but no desktop comes up. I only see a cursor arrow (at the correct resolution) on a black screen. Did the driver end up on the wrong graphics card? I can't go back and reinstall the 304.43 driver because I can't get into a shell and when I boot it using the recovery option, I'm told there's a problem writing to /tmp.
Distribution: Debian Sid AMD64, Raspbian Wheezy, Slackware Current AMD64, various VMs
It sounds to me like perhaps your desktop is being sent to another of your cards rather than the one with the monitor plugged in.
You could try switching to a text terminal and running nvidia-xconfig. This sound give you an xorg.conf which you could then edit if required. I had to use a similar technique when I ran two separate NVIDIA cards.