Explanation of Issue:The patch titled "11_2_l46_s6_ges_patch.zip" which was available in
(Xilinx Answer 33124) contains additional design files related to the Spartan-6 LX4 device family that were not included in the original install. The addition of these files causes EDK to result in a Fatal Error when attempting to open a new design targeting any Spartan-6 device.
Fix:To fix the issue, you must navigate into your ISE software installation and delete these additional Spartan-6 LX4 device files. This can be performed by going into your Xilinx installation in the Spartan-6 Data folder (typically C:\Xilinx\11.1\ISE\spartan6\data) and delete the files related to the Spartan-6 LX4 device. There are 12 files in all, which can be seen in the image below. After deleting the files, re-open EDK and everything should work correctly.

Spartan-6 LX4 device files to be removedInstalling ISE Design Suite 11.3 over the ISE Design Suite 11.2 with General ES patch will not fix this issue. You must manually delete the files as described above.
Issues might be seen with some of the other Xilinx tools, such as CORE Generator interface, when opening a Spartan-6 FPGA project with this patch installed. This is due to the same issue described above, so please proceed with the fix and your problem should be resolved.
If you have additional issues, please contact Xilinx Support:
http://www.xilinx.com/support