Problem of download the code in altera cyclone II kit.

Have you ever used tcl scripts?? I have the problem sometimes, and what I do is, I add all the standard pin assignments into my tcl script, and run it. So now, (after compilation) when you open the pin planner, every possible pin has an assignment. The you just change the pins that you are going to be using in the pin planner, and compile it again, and then the problem should hopefully go away.