You will see this message if you have enabled Base Address Registers (BARs) for the Avalon Memory-Mapped (Avalon-MM) of the Altera® Hard IP core for PCI Express® with Port type set to Native Endpoint, but then switch to Port type Root Port.
For example:
1) Enable BAR0 (32-bit non prefetchable)
2) Enable BAR1 (32-bit non prefetchable)
3) Change the Port Type from Native endpoint to Root port
To work around this issue:
Re-select the Endpoint type, disable all BARs, then re-select Root Port type.
This behavior is not scheduled to be changed in a future Quartus® II software version.