When GTX DUALs are used in an IBERT design in the second MGT column (X1Y*) in the TXT family, the Analyzer console is not reporting the location correctly. The transceiver still works, but the information is wrong. The clock forwarding combo box will not work properly.
This issue will be resolved in ChipScope Pro 11.1. There is a patch available targeting ChipScope Pro 10.1 Service Pack 3. The patch files can be downloaded at the following link:
http://www.xilinx.com/txpatches/pub/swhelp/ise10_updates/31857.zip