The 9.1i iMPACT software will run an IDCODE check on the SPI devices before programing them. The program operation will still complete although they IDCODE check fails.
This problem has been fixed in the latest 9.1i Service Pack available at:
<http://www.xilinx.com/xlnx/xil_sw_updates_home.jsp>
The first service pack containing the fix is 9.1i Service Pack 2.