The ISE 12.4 software contains production speed files for the Spartan-6 devices. The Spartan-6 -3 speed files increased in performance in 12.4, which means the new speed files do not match the Engineering Sample (ES) silicon.
Any designs targeting -3 ES silicon must follow the instructions below. Also, the SP605 evaluation board contains -3 speed grade devices. The initial production of these boards contained ES parts. Customers using the SP605 should visually inspect the part marking; if it contains an "ES", then follow the instructions below.