Virtex-4 allows the flexibility to change the default pull-up resistor on dedicated configuration pins, but this does not seem to be supported by the software.
This problem has been fixed in the latest 6.3i Service Pack available at:
The first service pack containing the fix is 6.3i Service Pack 2.
Several new "-g" options are associated with the dedicated configuration pins to support this hardware feature. These new options are:
InitPin Pullup, Pullnone
CsPin Pullup, Pulldown, Pullnone
DinPin Pullup, Pulldown, Pullnone
BusyPin Pullup, Pulldown, Pullnone
RdWrPin Pullup, Pulldown, Pullnone