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I managed to hack-fix this for now. All i did was just rebuilding pcl from ros-gbp/pcl-fuerte-release.git on github(debian/fuerte/precise/pcl branch) on the machine it's running on and then simply replacing the libpcl files in /opt/ros/fuerte/lib with the ones i built.

Not a clean fix as it interfers with the package manager, but it works for now and i hope that the next update fixes it.

It looks like cmake checks for the SSE and other cpu capabilitys when it's configuring. So if the buildservers are capable of avx and other extensions, that'd explain how the instructions got in there.