The Quartus® II software versions 9.1 SP1 and 9.1 SP2 will not compile the combination of VCCA = 2.5V with VCCL/R/T=1.2V for Stratix® IV GX designs.
When VCCL/T/R=1.2V is required to achevie a higher data rate on any transceivers, VCCL/T/R on both sides of the device are set to 1.2V. Also in VCCA Auto mode, VCCA is set to 2.5V if the data rate on that side is below 4.25G even though the VCCL/T/R is set to 1.2V. To compile the design succesfully, the VCCA needs to be set to 3.0V on both sides.
Figure 1 : Megawizard™ pull down for VCCA selection
Figure 2: Example Design that won't compile without VCCA = 3.0.
The Stratix IV GX device does not require the higher VCCA if the data rate is below 4.25G on that side. This is a software issue which will be fixed in a future version of Quartus II software.