Quartus® II incorrectly assigns I/O standard for the refclk pin on Arria® II GX/GZ and Stratix® IV GX/GT devices for ALTGX instances, if you do not manually assign the correct refclk I/O standard for the pll_inclk port. Quartus II auto-assigns the general default I/O standard set by user in the design. This leads to an incorrect setting of the I/O standard of 2.5V to the REFCLK pin.
Device Family: Arria® II GX
Device Family: Arria® II GZ
Device Family: Stratix® IV
Manually assign the correct refclk IO standard for the pll_inclk pin.
This issue will be fixed in future Quartus II release.