When there is only one Virtex-4 device in the chain, iMPACT fails to program the device. The DONE pin goes High and iMPACT reports that programming has succeeded. When a Read Status Register is performed, the GHIGH bit will be set to 0. This problem is unique to Service Pack 3.
This problem will be fixed in the next release of the software.
In the meantime, install the patch found in (Xilinx Answer 21694) over Service Pack 3.