Due to a bug in the Quartus® II software version 13.0 and earlier, you may see transceiver functionality problems on Stratix® V, Arria® V, or Cyclone® V transceiver devices.
The transceiver reconfiguration controller can have incorrect initial state which may cause transceiver functional problem.
The transceiver can be recovered by resetting the transceiver without power cycle.
To ensure correct initial state of reconfiguration controller, you can add QSF assignments below.
set_instance_assignment -name POWER_UP_LEVEL HIGH -to *pif_interface_sel
set_instance_assignment -name POWER_UP_LEVEL HIGH -to *pif_ser_shift_load
This problem will be fixed in a future version of the Quartus II software.