There is a known issue in the ISE 11.4 software with calculating the CRC value for SEU detection (POST_CRC). There is no work-around in the current software. The issue is fixed in the ISE 11.5 software and later versions.
Refer to the Spartan-6 FPGA Errata page for the Spartan-6 device which you are using. None of the ES (Engineering Sample) devices support POST_CRC, so the software issue is irrelevant in those cases. The Production status devices do support POST_CRC, so ISE 11.5 software should be used with those devices to fully support the POST_CRC solution.