The PCI Express Compiler v10.0 does not support IP and MegaWizard generation or regeneration of PCIe Gen1 x4 or x8 designs targeting the Stratix IV GX, Stratix IV GT, and HardCopy IV device families.
The workaround is to upgrade to version 10.0 SP1 or 10.1 of the Quartus II software.
A second alternative is to continue to use the Quartus II 9.1 SP2 release to generate the affected Gen1 PCI Express variation. After generating your variation using the Quartus II 9.1 SP2 software, you can compile the complete design using the Quartus II v9.1 SP2 or v10.0 software release.
A third alternative is to parameterize the PCI Express MegaCore function to run at the Gen2 rate.
This issue is fixed in version 10.0 SP1 of the PCI Express MegaCore function.