Why does my Arria V or Cyclone V Avalon-MM configuration of PCI Express fail to link train correctly?

After Qsys generation has completed, manually modify the following files found in the folder <Qsys System>\synthesis\submodules\

altpcie_av_hip_ast_hwtcl.v and altpcie_cv_hip_ast_hwtcl.v

Change from:
      parameter rpre_emph_a_val_hwtcl                             = 0,
      parameter rpre_emph_b_val_hwtcl                             = 0,
      parameter rpre_emph_c_val_hwtcl                             = 0,
      parameter rpre_emph_d_val_hwtcl                             = 0,
      parameter rpre_emph_e_val_hwtcl                             = 0,
      parameter rvod_sel_a_val_hwtcl                              = 0,
      parameter rvod_sel_b_val_hwtcl                              = 0,
      parameter rvod_sel_c_val_hwtcl                              = 0,
      parameter rvod_sel_d_val_hwtcl                              = 0,
      parameter rvod_sel_e_val_hwtcl                              = 0
To:
      parameter rpre_emph_a_val_hwtcl                             = 6\'b000000,
      parameter rpre_emph_b_val_hwtcl                             = 6\'b000000,
      parameter rpre_emph_c_val_hwtcl                             = 6\'b010000,
      parameter rpre_emph_d_val_hwtcl                             = 6\'b001100,
      parameter rpre_emph_e_val_hwtcl                             = 6\'b000101,
      parameter rvod_sel_a_val_hwtcl                              = 6\'b101001,
      parameter rvod_sel_b_val_hwtcl                              = 6\'b100111,
      parameter rvod_sel_c_val_hwtcl                              = 6\'b100101,
      parameter rvod_sel_d_val_hwtcl                              = 6\'b100111,
      parameter rvod_sel_e_val_hwtcl                              = 6\'b001111

This issue is scheduled to be fixed in a future version of the Quartus II Software.