In 5.1i with Service Pack 3, the CPLD JEDEC file generator (Hprep6) assigns unused pins to float regardless of the termination setting in the ISE GUI. If I terminate unused pins to a keeper or pull-up in the GUI or command line (cpldfit), Hprep6 still leaves the unused pins floating.
This problem is due to a bug that was introduced in 5.1i Service Pack 3.
This problem is fixed in the latest 5.2i Service Pack available at:
The first service pack containing the fix is 5.2i Service Pack 2.