For any setting of TXDIFFCTRL, 12.3 IBERT and earlier generates TX differential swing numbers that are below what is in the Virtex-6 FPGA GTX User Guide and Characterization Report, and whatisoutput by designs generated by the Virtex-6 FPGA GTX Transceiver Wizard.
The reason for this inconsistency is an incorrect setting on the TXBUFDIFFCTRL port. The current value is 3'b010 and should be updated to 3'b100 as recommended by the Virtex-6 FPGA GTX User Guide. This can be done directly in the IBERT GUI under the Ports and Attributes tab. This issue will be resolved in ChipScope tool 13.2.