When the Xinfo System Checker tool is launched, the value of the $PATH variable does not match the settings specified by the system.
The Xilinx implementation and analysis tools use a 'bootloader" mechanism at start-up to ensure that their environment variables are properly configured. This mechanism automatically inserts references to the Xilinx tools installation directory.
In order to properly reflect the environment in which the tools will find themselves at start-up, the Xinfo System Checker tool is also "bootloaded". Thus, in certain configurations, it is possible that the data reported by the Xinfo tool will reflect these paths, even if they are not actually set in the system's variables. This is normal and expected behavior.
In order to have the Xinfo System Checker tool report the exact system state (with no modification whatsoever), run the _xinfo tool rather than the xinfo tool.