You may see this warning when compiling a Stratix® V GX Native PHY IP in Quartus II software version 12.0 SP2 and earlier when generating MIF files for the dynamic reconfiguration feature. This warning can safely be ignored.
Device Family: Arria® V GX, Stratix® V, Stratix® V GX
Area: Component, HSIO
This issue will be fixed in a future version of the Quartus II Software.