When creating an IPI design there is an issue when write_bd_tcl generated set_property list for processing_system does not set all properties. If the generated Tcl script is sourced in new project, some of the MIO settings are missing in the new project.
The Processing_system IP is not correctly using the Tcl constrains for the MIO.
To work around this issue for 2013.2, import an XML file generated from XPS.
This issue has been fixed in Vivado Design Suite 2013.3.