The compile order of XDC constraint files is not added to the Tcl file generated with "write_project_tcl".
After restoring a project with the generated Tcl file, the constraints can be in a different order which can cause the run to fail or have different results.
This issue has been corrected in Vivado 2014.1.
A workaround in Vivado 2013.4 is to edit the Tcl generated by the write_project_tcl command to manually change the order in which the file are loaded into the project.
In the constraints section, change the order of the files in the sections below.
This will set the order of the constraints when the project is opened again: