In the Clocking Buffers window in the Clocking Wizard, I can select an I0 or I1 input from the DCM output or CLKIN. However, the non-default selection is lost after I reopen the ".xaw" file -- the Clocking Wizard resets the changes to the default settings.
This problem has been fixed in the latest 6.1i Service Pack, available at:
The first service pack containing the fix is 6.1i Service Pack 1.
The Clocking Wizard now saves the user selection.