Hi,
1-- Can you also test the voltage of nCSO with blank FLASH?
2-- Please check if the nSTATUS pin of good and faulty board has same connection/settings.
It seems that the nSTATUS signal of "Good" and "Faulty" Boards starts with different voltage level. As you know, the nSTATUS and nCONFIG need be connected to pull-up resisteor, which means they should start with High.
3-- Are all boards successfully configured with SOF through JTAG?
As for your question about nSTATUS, only CONFIGE_DONE signal reflects the success of JTAG configuration. Therefore, you do not need to test nSTATUS and nCONFIG signals during the JTAG config, and the trigger signal for oscilloscope should be CONF_DONE.
4-- If the faulty board is successful in JTAG Config, and the board connection/software settings are the same as the good ones, we may suspect the nCSO pin defect.
Regards,
Xiaoyan