It is not possible to connect the transceiver reconfig_to/from_xcvr ports between the reconfiguration controller and the 1G/10GbE and 10GBASE-KR PHY IP in QSYS on Stratix® V GX devices due to a bug in the Quartus® II software versions 12.1 and earlier.
To work around this problem, export the reconfig_to/from_xcvr ports of the transceiver Reconfiguration Controller and the 1G/10GbE and 10GBASE-KR PHY IP and connect in your RTL.
This issue will be fixed in a future version of the Quartus II software.