In the Quartus® II software version 6.1, the .pin file incorrectly shows VCCA power pin values based on the Bank1 I/O standard. For example, if you assign an I/O standard of HSTL class II 1.5V to a pin in Bank1, the .pin file shows 1.5V for the VCCA pin. The VCCA pin values should be 3.3V and do not depend on the Bank1 I/O standard.
This issue has been fixed beginning with the Quartus II software version 7.0.
To work around the issue in the Quartus II software version 6.1, install the appropriate patch from the following list: