Yes, due to an Assembler bug in Quartus® II 9.1SP2 and earlier versions, the configuration files contain only the default setting for on-chip clamp diodes on column I/O pins regardless of the logic option “PCI_IO” setting. The affected device families are: Stratix® III, Stratix IV, Hardcopy® III, Hardcopy IV and Arria® II GX devices.
For PCI/PCI-X I/O standards, the on-chip clamp diode is always enabled. There is no impact on 3.0V PCI/PCI-X IO pins since the on-chip clamp diode is always enabled to protect the IO buffer from overshoot voltage.
For the 3.3V/3.0V LVTTL/LVCMOS I/O standards, the on-chip clamp diode is always disabled. You could opt for an external clamp diode solution.
You can verify if you are impacted by the Assembler bug by comparing two .sof files (configuration files) of same design which is compiled by same Quartus II software version but with different settings of the on-chip clamp diode. If the two files do not have a binary bit difference, you are impacted by this bug.
The Assembler bug will be fixed in a future version of the Quartus II software. If you need to control the on-chip clamp diode at this time, you can install Quartus II 9.1 SP2 and apply Linux or PC patch 2.06.
Quartus II software version 9.1 SP2 Linux Patch 2.06
Quartus II software version 9.1 SP2 Windows Patch 2.06
You must note that the ReadMe file contains an INI variable that needs to be set along with installing Quartus II software version 9.1 SP2 and patch 2.06.
You can create a Quartus II .ini file using Notepad. Launch Notepad and copy the INI variable into the file. Select: File>Save As and name the file, "quartus.ini" and change the "Save as type" to "All Files" and save the file into your project directory.
If you do not change the "Save as type" to "All Files", Notepad will add and extension of .txt to the file name. This will cause the Quartus II software to not read the quartus.ini file and implement the INI variable properly.