There are multiple DRCs (Design Rule Checks) not implemented in the ISE Design Suite 11.2 software for Spartan-6.
Many of these DRCs are related to the IOLOGIC functionality of the Spartan-6 devices. If you are using ISERDES, OSERDES, ILOGIC, OLOGIC, or IODELAY, there might be checks missing from the existing software, specifically related to placement and routing. DRCs are being added to software and will be available in the next version of ISE Design Suite.
It is strongly suggested that every design be re-implemented in the next version of ISE Design Suite software when it becomes available.