If you migrate from one version of the Quartus® II software to another version, the files in the /db folder will not be updated if you make changes to the PLL settings in the ALTPLL megafunction. In order for your changes to take affect, you need to delete both /db and /incremental_db folders in your project directory, then regenerate the ALTPLL megafunction for your design.
You can verify the changes are correct by looking at the PLL Usage Panel in the Compilation Report => Fitter => Resource Section.