The (non AXI) PCI Express endpoint of the Virtex 6 can be rendered inaccessible after a PME_turn_off command (from a CPU reboot). A core reset was added to the pcie_interface.vhd as a workaround in that situation with minor firmware revision 0x0E.
The ready to use PROM files for the DWC and SIS8900 versions can be dowloaded from:
URLs for the macro versions will be emailed on request.
We would like to thank the team at N.A.T for the support in locating the issue and testing the workaround implementation.