On prior families the PROG or the INIT pins can be held low at power-up to delay configuration. With the Virtex-6 devices the PROG pin is edge sensitive as opposed to level sensitive. So, holding this pin low at power up will not continue to delay configuration.
The way to delay configuration is to hold the INIT pin low. INIT is an open drain driver and requires a pullup on the pin to pull the pin high once it is released by the device. The device will only drive the pin low, and will then release the pin when the device is ready to start configuration. The INIT pin must then go high for the mode pins to be sampled and the configuration process to begin.