saving changes from pin planner

You don't have the .qsf open in an application that locks it and prevents the Quartus Pin Planner from writing to it, do you? Yes, the .qsf is updated on the fly from the Pin Planner, or when you close the Pin Planner. Make sure Quartus is free to write to the .qsf. I've not had any problems of this nature for a long time - and those I did have proved to be of my own making...