The lower level primitive (PS7) has pins tied to upper levels, but then levels above the pins are unconnected.
Instead of leaving the pins of the primitive unconnected, the tool ties off the upper level to 0, and then does constant prop all the way down to the primitive.
Use the parameter below in the Tcl console before running Synthesis and Implementation in Vivado 2013.4.
set_param synth.elaboration.rodinMoreOptions "rt::set_parameter retainUnconnectedPinsForPrimBBox true"
This parameter tells the tool to retain the Unconnected pins for Xilinx Primitives and Black Boxes, and not to connect it to 0.