When using the IBERT core for Virtex-6, Virtex-7, and Kintex-7 devices, a USB cable speed of 12 MHz will not work correctly. The following AR discusses this issue in detail.
The IBERT design for the Virtex-6, Virtex-7, and Kintex-7 devices has a design limitation which will not work with 12 MHz USB cable speeds. The behavior you will observe is inconsistentfunctionality.This design limitation will be fixed in ISE 14.1 software for the Virtex-7 and Kintex-7 devices. No fixes for the Virtex-6 IBERT core are planned at this time.
To work around the issue, select a cable speed of 8 MHz or below.