When using calibrated On Chip Termination (OCT) in Stratix® II and Stratix II GX devices, you will receive this warning when using Quartus® II software version 6.1 and above.
Stratix III devices have a different OCT calibration circuit than Stratix II devices and were first supported in Quartus II software version 6.1. In Stratix III devices, I/O pins can use different OCT calibration blocks and must be assigned appropriately.
Stratix II devices have two OCT calibration blocks, one for the top I/O banks and one for the bottom I/O banks. The Quartus II software will automatically use the correct OCT calibration blocks for Stratix II devices.
These warnings can be safely ignored for Stratix II designs.