Are the PCI and PCI-X LogiCORE cores supported in the Modular Design flow?
The PCI and PCI-X LogiCORES are not supported in Modular Design. This is because of the cores' use of instantiated IOBUF primitives in the cores themselves.
Modular Design expects that all INOUT ports will result in internal TBUF elements, and this is not compatible with PCI and PCI-X LogiCORE. PCI and PCI-X LogiCORE support is planned for a future release.