Due to a bug in Quartus® II software versions 13.0, 13.0sp1. 13.1, and 13.1sp1 you may see an increase in measured transceiver VCCL_GXB and VCCR_GXB current for Cyclone® V, Arria® V, and Stratix® V transceiver devices.
The increase in measured VCCL_GXB and VCCR_GXB current is dependent upon the number of unused dedicated transceiver REFCLK pins in your design, and whether they are connected directly to GND as defined in the device Pin Connections Guidelines document.
For example: A design with more unused dedicated REFCLK pins that are tied directly to GND will require more current than a design that has fewer unused dedicated REFCLK pins connected directly to GND.
Connecting unused dedicated REFCLK pins to GND through a resistor will reduce any possible current increase and will not affect the behaviour of the device.
This problem will be fixed in a future version of the Quartus II software.
You can contact Altera Support for further help on this problem.