To work around this issue, manually changing the QPLLREFCLKSEL port to the correct value will be necessary so the proper reference clock is used by the design.
Follow these steps to make the necessary change:
At this point, it is possible that the QPLL still shows that the QPLL is not locked, but the GTX should now show LINKED. This is a known issue in 13.3 which is caused by the IBERT Core not reading the currentvalue of the QPLL locked status periodically. Follow the steps in (Xilinx Answer 44649) which details how to force IBERT to read the proper status of the QPLL Locked field.
This is a known issue in 13.3 and is scheduled to be fixed in 13.4.