Arria V SoC HPS EMAC 1588 PTP Feature

If in Qsys I connect hps_0.emac_tx_clk_in and hps_0.emac_ptp_ref_clock up to the reference clock from my design, the design compiles and there is still a functional Ethernet, despite all of the new Ethernet signals which show up as a consequence of making the above changes, so there doesn't seem to be a need to deal specially with these signals. The problem now, however, is that Qsys reports my drive signal for hps_0.emac_ptp_ref_clock and hps_0.emac_tx_clk_in with the warning "Interface has no signals," even though they are clearly connected to my drive signal. The result in the post-fit netlist viewer has no string "ptp_ref_clock" in it, so I'm missing something in ensuring connectivity. Soc_system/synthesis/soc_system.vhd contains the line