The Quartus® II software version 9.0 incorrectly allows you to set the programmable weak pull-up resistor logic option on dedicated clock input pins for designs targeting Arria® II GX devices and reports this option as enabled in the compilation report file.
There is no programmable weak pull-up resistor available for dedicated clock input pins during user mode operation. The programmable weak pull-up resistor is only supported on user I/O pins for Arria II GX devices as stated in I/O Features of Arria II GX Devices (PDF).
This problem is due to be fixed in a future version of the Quartus II software.