After I create a timegrp in the editor, it does not appear in the New Input/Output Wizard dialog, but does appear in the Register timegrp dialog.
To work around this issue, manually edit the UCF. Or, you can create pad groups using Group by Element type.
This problem has been fixed in the latest 10.1 Service Pack available at:
http://www.xilinx.com/support/download/index.htm
The first service pack containing the fix is 10.1 Service Pack 1.