Yes, for Stratix® III devices, the Quartus® II design software versions 7.2 SP1 and earlier incorrectly report the VCCPD voltage in the Pin-Out file (.pin) as 2.5 V for any I/O bank with the VCCIO set to 3.3V.
If the VCCIO of an I/O bank is set to 3.3 V, the VCCPD requirement is 3.3 V. If the VCCIO of an I/O bank is set to 3.0 V, the VCCPD requirement is 3.0 V. If the VCCIO of an I/O bank is 2.5V or lower, the VCCPD requirement is 2.5V.
This problem is fixed beginning with the Quartus II software version 7.2 SP2.