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 70C or higher, occasional Rx bit errors may be seen due to an incorrect CDR setting when the transceiver is configured for datarates of >2Gbps and <2.5Gbps. 2Gbps and 2.5Gbps are not affected. The bit errors may be continuous or random.
To fix this issue upgrade to Quartus II software version 12.0SP2 or later, regenerate your ALTGX transceivers, and recompile.