The iMPACT Indirect BPI programming core upper address bits are dual mode and hence are also Vref pins for the bank. These upper address bits are always driven by the core design even when target flash does not use all the Address pins. Vref, when used, can be driven by a power source, so contention may occur while the address lines drive low.
You may see this on the smaller LX devices where you can use a smaller flash:
FG(G)484 Package - LX25, LX45, LX75, LX100, and LX150
IO_L1N_A24_VREF_1_B20
CSG225 Package - LX9 and LX16
IO_L1N_A24_VREF_1_B15
FT(G)256 Package - LX9, LX16, and LX25
IO_L1N_A24_VREF_1 _E12
Vref should not be used for configuration banks on Virtex-6 FPGA if using Indirect BPI programming.