When running "Create Timing Constraints" in ISE, I select "Show constraints from specified file only", and select "top.ucf" for the top module. Correct "Pad to Pad" constraints are displayed. When I select a different UCF file, "more_timing.ucf" for a submodule, the "clk" specs are correctly loaded. However, "Pad to Pad" is still displayed in the UCF text view.
This problem has been fixed in the latest 10.1 Service Pack available at:
The first service pack containing the fix is 10.1 Service Pack 1.