If you have set up your DDR3 HP Controller IP Megawizard® "Auto-Calibration Simulation Options" in "Skip Calibration" mode, in the simulation you will see the CWL of 5 even if you have set the CWL parameter to 6 in the IP Megawizard.
The Quartus® II software and IP version 8.1 and earlier only support CWL of 5 for "Skip Calibration" mode.
Change the setting for "Auto-Calibration Simulation Options" to "Quick Calibration" or "Full Calibration" mode to get correct CWL value of 6 in the simulation.
This issue will be fixed in the future version of the IP and Quartus II software.