By default, the input buffers are turned off for I/O pins that are configured as outputs in your MAX® II device.
To regenerate your programming file to enable the input buffers, you need to set the 'Always Enable Input Buffers' option in the Quartus® II software and re-run the Assembler.
This option is in the Assembler section under the Assignments/Settings menu in the Quartus II software.
For more information, refer to the BST for Programmed Devices section in IEEE 1149.1 (JTAG) Boundary-Scan Testing for MAX II Devices (PDF).