Is there a known issue with the Flash Chip Select setting in the Generic Serial Flash Interface Intel® FPGA IP when Advanced Mode is enabled?

Yes, due to a problem in Intel® Quartus® Prime Pro Edition Software version 22.2 and earlier, when Advanced Mode is enabled in the Generic Serial Flash Interface Intel® FPGA IP, the Flash Chip Select setting is not being mapped correctly to the Control Register bits [7:4]

For example, when the Flash Chip Select is set to '1', rather than the Control Register bits [7:4] being set to '000', a bit setting of '001' is being applied.

To avoid this issue, disable Advanced Mode.

This problem is expected to be fixed in a future release of the Intel® Quartus® Prime Pro Edition Software