This is due to a mistake in the tcl file that controls the GUI customization options. The easiest way to fix this is to download a new tcl file found at:
http://www.xilinx.com/txpatches/pub/applications/pci/ar36048.zip Place this file in the directory:
[XILINX Install Path]/ISE/coregen/ip/xilinx/network/com/xilinx/ip/v6_pcie_v1_5/gui/
Overwrite the existing v6_pcie_v1_5.tcl file and this enables you to generate a x8 Gen 2 design when targeting the XC6VLX365-3 part.
Revision History
06/04/2010 - Initial Release