Hi,
Is the CONF_DONE signal is directly pull up to the VCCPGM via 10kohm? If you have any other component such as LED or external host connecting to the CONF_DONE, remove those component. Potentially these extra component can hold the CONF_DONE low. Ensure the CONF_DONE signal is connected to VCCPMG via 10kohm pull up.
Are you using EPCQ128 or EPCQ128A? Did you try to perform ASx4 mode or ASx1 mode? If the ASx4 mode failed then try to change Active Serialx1 mode in the Device and Pin option in the Quartus project design can recompile to get new .sof file. Generate a new .jic and program it into the flash device and monitor if the configuration still fail (CONF_DONE low) or successful (CONF_DONE high).
Regards,
Nooraini