The PCI Express® tcl file "altera_pcie_avgz_hip_avmm_hw.tcl" found in the Quartus® II install directory: \altera\<your_version>\ip\altera\altera_pcie\altera_pcie_avgz_hip_avmm\ is missing the enable_hip_status such that the features are always enabled.
The following lines need to be added after the set enable_hip_status_ext section to ensure the Hard IP Status Bus can be enabled and disabled:
set enable_hip_status [ get_parameter_value CG_ENABLE_HIP_STATUS ]
if { == 1 } {
add_pcie_hip_port_status
}
This problem has been fixed in Quartus® II Software Version 14.0.