I installed the Linux version of CCSv5.1 (Build CCS5.1.0.07001_linux) from a command line in my user account. When I tried to build my project from within the eclipse system, I got a permission error when the make system tried to access /opt/ti/xdctools_3_22_02_27/xs.
Upon investigation, it seems that all of the files in the xdctools_3_22_02_07 directory and its subdirectories do not have execute permissions. I had to chmod -R oug+x xdctools_3_22_02_27 to get the build to work.