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No problem for that under Ubuntu, they install to /opt/ros/fuerte and /opt/ros/groovy respectively, on purpose.

With two distros, it is usually safest to not source any setup.sh in your .bashrc, but to source the respective setup.sh per terminal, and not switch during that session. generally switching can work, but there can be undesired side-effects.

Also for writing your custom code, it is also safer to have separate source files (workspaces), unless you know well what you are doing.