In Intel® Quartus® Prime software version 18.1 and earlier, the "Disable EPCS/EPCQ ID check" setting is unchecked by default which causes the configuration control block in the FPGA to only recognize the ID from EPCS/EPCQ serial configuration flash devices.
This results in the FPGA not being able to configure from a Macronix* MX25U or MX66U Flash device after power cycle even though the programming of the flash is 100% successful.
To work around this problem, check the "Disable EPCS/EPCQ ID check" setting under “Advanced...” setting in Convert Programming Files.