An iMPACT-generated system ACE CF file does not program a Spartan-3 device if 6.2 is being used. The problem has also been seen with the 8.1 and 8.1.01 releases of the software. Design files will download to the devices from iMPACT, but the .ace file will not work on the chain. The problem is a result of a switch missing in the software.
To work around this problem, manually run SVF2ACE with the "-wtck" option. You can download the SVF2ACE utility from:
http://www.xilinx.com/txpatches/pub/swhelp/ise5_updates/svf2ace.zip
This problem has been fixed in the latest 6.2i Service Pack, available at:
http://support.xilinx.com/xlnx/xil_sw_updates_home.jsp
The first service pack containing the fix is 6.2i Service Pack 1.
This problem has also been fixed in the latest 8.1i Service Pack, available at:
http://support.xilinx.com/xlnx/xil_sw_updates_home.jsp
The first service pack containing the fix is 8.1i Service Pack 2.