This message occurs because the Quartus® II software allows the PCI clamp diode to be enabled only for I/O pins that use a 3.3V I/O standard.
To work around this restriction for input pins in 2.5V I/O banks, define the pin as a 3.3V I/O standard. This is permitted because 3.3V inputs are allowed in a 2.5V I/O bank. The software successfully compiles the design resulting in an input pin with a 2.5 V clamping diode. Altera® does not support this application because the PCI clamp diode is intended only for use in a 3.3V I/O standard. There are no plans to provide IBIS models for this implementation.
Beginning with version 7.1, the Quartus II software message is improved for this case.