the problem of programming the PCIe pex_exmaple_design

Use a text editor to open up the quartus settings file (*.qsf) of your project and of the PCI Express High Performance Reference, and compare the two. There may be assignments in the reference design that may help your own project.

Also, what Quartus version are you using? My Arria GX development board came with Quartus 7.2, and the reference design was written in 7.2 as well. However, whenever I attempted to duplicate the reference design in 8.0 or 8.1, I would experience multiple problems with my computer at startup. I very much recommend using the latest versions of Quartus, as bugs that appear in earlier versions have since been fixed. Try designing a project in Quartus 9.0.