Hi,
1-- nCS settings
By comparing the waveform of nSTATUS and nCS of the fault board, it seems the configuration failure is caused by the nCS signal being abnormally pulled high.
When nCS cannot be pulled low, AS configuration cannot be started, so that DCLK and nSTATUS signals are not correct.
Please check if there's difference in the nCSO pin between "Good" and "Faulty" boards, including the board connections, settings in Quartus.
2-- Good board's CONFIG_DONE is low, which indicates the Configuration is not done. How do you confirm that those ones are successfully configured? Are you just keep making the FPGA restart configuration?
3-- Can you capture the waveform with all these signals showing in the same screen? From the POR to the time failure happens.
Thanks & Regards,
Xiaoyan