Due to a bug in the Quartus® II software version 12.0SP1 and earlier, you might see occasional temperature dependent bit errors on Cyclone® IV GX Rx transceiver channels.
When the device junction temperature is approximately 70°C or higher, occasional RX bit errors might be seen due to an incorrect CDR setting when the transceiver is configured for data rates of >2 Gbps and <2.5 Gbps. 2 Gbps, and 2.5 Gbps are not affected. The bit errors mihgt be continuous or random.
To fix this problem, upgrade to Quartus II software version 12.0SP2 or later, regenerate your ALTGX transceivers and recompile.