When entering a constraint into memory from the Tcl console and then clicking the "Save Constraints" GUI button, the constraint may not be saved in the same order that it was entered into memory via the command line.
To fully validate these constraints, they must be saved and then the design must be reloaded before running Synthesis or Implementation.
This is a known feature of the Vivado design tools.
In Vivado 2013.3, the following message has been added to notify the user of a possible constraint order change.
Window title: Constraints Order Changed
Text: All new constraints are saved to the target constraint file "xxx.xdc" in constraint set 'yyy' which is not last in the constraints compile order. The constraints sequence on file will not match the current sequence in memory. You must validate that the saved constraints still apply correctly by reloading the design and re-validating the constraints before running synthesis or implementation.