Virtex-6 FPGA GTH Transceiver Wizard v1.9 sets the PMA_LPBK_CTRL_LANEx[1:0] to 2'b10 by default.
As documented in Table 2-15 of the
Virtex-6 FPGA GTH Transceivers User Guide (UG371), this value sets the GTH Transceiver in TX pre-driver PMA loopback mode:
http://www.xilinx.com/support/documentation/user_guides/ug371.pdf To disable the loopback mode, this value should be changed to 2'b00.
This is fixed in v1.10 of the Virtex-6 FPGA GTH Transceiver Wizard released with ISE Design Suite 13.4.