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Just to be sure, 'roscd roscpp' does work for you? And you have sourced all setup.bash-es as needed?

I've had similar issues, though related to messages that catkin thought to be defined twice after I've installed rosjava from source into my workspace. What worked for me was to install rosjava into a separate catkin workspace, i.e. to chain two workspaces as described here. My layout was thus

~/ros/system_pkgs/src/rosjava etc <-- refers to /opt/ros/indigo/...
~/ros/custom_pkgs/src/knowrob etc <-- refers to system_pkgs workspace