All VCC_CLKIN supplies require 2.5V sources when used to power the transceiver REFCLK input pins. The REFCLK pins are powered by these dedicated VCC_CLKIN3A, VCC_CLKIN3B, VCC_CLKIN8A, and VCC_CLKIN8B power supplies separately in their respective I/O banks.
When REFCLK pins are assigned to the supported I/O standarads such as 1.5 PCML I/O standard in Quartus® II software version beginning with 11.0, the Fitter reports invalid VCC_CLKIN level. This is a software bug.
Please make sure that the VCC_CLKIN supplies are tied to 2.5V source on your board.
This issue is not observed if you are using a Quartus II software version eariler than 11.0.
This issue is resolved in the Quartus II software version 12.1.