This is a Windows only issue.
When SysGen is launched properly (from the Start menu), it sets up the Xilinx environment for you, partially based on the settings that you set in the Configurator. It simply appends the configured versions of Matlab onto the front of your path. When multiple versions of Matlab are configured, it appends both versions in numerical order. The older version may be appended first in the path, thus SysGen will find and use the older version.
You can manually unconfigure Matlab by modifying the followingthree files:
For System Generator for DSP Release Notes from other versions, see (Xilinx Answer 29595).