I setup MSEL for parallel programming (as described in a user guide) I download a firmware into a flash memory with special design, it was presented by terasic. My firmware downloaded is correct (i can run a signaltap that included in a design). The same board with the same firmware load correctly with i7 processor and windows OS.
Now I can run a firmware after reset: I power up a PC, after it run I doesn see a PCIe device and after reset without power down PCIe links correctly setup. For this I change settings in PCIe controller "Endpoint L0 and L1 acceptable latency on a no limit.