The Virtex-5 devices can be used to indirectly program a Flash device in iMPACT. On occasion the software does not display the Flash icon in the GUI after the device has been added. To see the Flash device, right click in the GUI where the device should appear.
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.