Your Arria® V, Cyclone® V, or Stratix® V device Transceiver Toolkit design may show a greyed out System Console panel when using Quartus® II software version 14.0 if there isn't a transceiver PHY at address 0x0000 of the QSYS memory map.
To work around this problem, open your transceiver toolkit design QSYS system and place your first transceiver PHY IP at address 0x0000.
After placing your transceiver PHY IP at QSYS address 0x0000 you must recompile your Quartus II project.