General Description: The default value for "Unused IOB pins" under Configuration Options in the 4.2i and 5.1i ISE software GUI is "Pull-up". However, the Xilinx online software manuals state that "the default setting for unused pins is Pull-down."
If BitGen is run from a command line, the default value for "Unused IOB pins" (-g UnusedPin) is "Pull-down". The default value for "Unused IOB pins" in the 4.2i and 5.1i ISE GUIs should be changed to "Pull-down".
This will be changed in the 6.1i software release; until then, manually change the property to the desired value for your current project.