I have never used a PCI-E-attached Cyclone V board but for PCI-E-attached Stratix V and Arria 10 boards, after the initial programming via JTAG to enable the PCI-E core, the JTAG cable will not be required anymore (unless the PCI-E core breaks and JTAG reconfiguration is required again). Since diagnose is passing in your case, PCI-E transfer must be working correctly. However, for some reason, run-time FPGA reconfiguration seems to be going through JTAG instead of PCI-E. Unless Cyclone V does not support PCI-E-based reconfiguration, this should not happen.