Does the non-volatile configuration register need to be set when a Micron QSPI flash ROM device is used for Intel® FPGA Parallel Flash Loader II IP?

Yes.  When a Micron QSPI flash ROM device is used for the Intel® FPGA Parallel Flash Loader II (PFL II) IP and 3rd party programmer or user’s solution is used to program a programming file to the QSPI flash ROM device, the 16-bit non-volatile configuration register (NVCR) of the QSPI flash ROM device needs to be set to 0xFFEE manually. This setting disables the reset/hold feature on DQ3, enables 4-byte address mode, and leaves the other settings default.

.When the Quartus Prime Programmer is used to program a Micron QSPI flash ROM for the Intel® FPGA PFL II IP, the NVCR is automatically set to 0xFFEE during programming a programming file.