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The differences you list are significant, and could certainly be responsible for your issues. Without more information, it is unlikely that anyone will be able to help. Things you could try to identify or workaround the issue:

1. Try different drivers for your graphics card. In my own experiences, I've had terrible luck with AMD cards and Linux. I often run into issues with the drivers provided by fglrx or fglrx-updates, and the performance of the radeon drivers leaves something to be desired. The Ubuntu wiki has a pretty good tutorial on switching to various versions of the fglrx drivers. If you're already using fglrx you could revert to the radeon drivers.
2. You could fallback to using your CPU's built-in graphics.
3. Try disconnecting the second monitor. I have encountered issues in the past where multiple monitors cause issues. If this fixes the issue, it is possible that different settings in your Xorg.conf file would allow you to use both monitors with your ATI card.

The differences you list are significant, and could certainly be responsible for your issues. Without more information, it is unlikely that anyone will be able to help. Things you could try to identify or workaround the issue:

1. Try different drivers for your graphics card. In my own experiences, I've had terrible luck with AMD cards and Linux. I often run into issues with the drivers provided by fglrx or fglrx-updates, and the performance of the radeon drivers leaves something to be desired. The Ubuntu wiki has a pretty good tutorial on switching to various versions of the fglrx drivers. If you're already using fglrx you could revert to the radeon drivers.
2. You could fallback to using your CPU's built-in graphics.
3. Try disconnecting the second monitor. I have encountered issues in the past where multiple monitors cause issues. If this fixes the issue, it is possible that different settings in your Xorg.conf file would allow you to use both monitors with your ATI card.
4. It seems odd that you would get no messages of any kind when you run rviz. If you can obtain some sort of error logs, backtraces, something, it would help people narrow down your errors. If you're really not getting anything in your terminal, you could try looking at dmesg for possible issues. There may be messages printed to /var/log/ files. You could try running rviz in gdb with a command like gdb -ex run /opt/ros/indigo/lib/rviz/rviz