When I implement a PCI-X core in the 6.1i software, the following warnings are reported during NGDBuild:
"WARNING:NgdBuild:440 - FF primitive 'XPCI_WRAP/XPCI_CORE/XPCI_PAR64C' has an unconnected output pin."
"WARNING:NgdBuild:440 - FF primitive 'XPCI_WRAP/XPCI_CORE/XPCI_PARC' has an unconnected output pin."
These warnings may be safely ignored. They are an artifact of the "KEEP" attributes on some of the nets, which have preserved certain buffers inside the core for hold time reasons.