There is a PULLUP on the output net of a design (NGD file). If this PULLUP constraint is not in the UCF, then it is not displayed in the Constraints Editor window. (If this constraint is in the UCF, then it is displayed.)
Having the constraint in either the NGD file or the UCF will achieve the same results; however, the constraint may or may not appear in the Constraints Editor. Therefore, we recommend that you use the UCF, so that the constraint is visible and can be easily modified.
This is fixed in a future software release or service pack.