Description
Due to a problem in the Intel® Quartus® Prime Pro Edition Software v21.2, the JTAG user code is greyed out in the Device and Pin Options pane even if you uncheck Auto user code.
Resolution
To work around this problem, modify the JTAG user code by using the following assignment:
set_global_assignment -name STRATIX_JTAG_USER_CODE <JTAG user code>
This problem is fixed beginning with v21.3 of the Intel® Quartus® Prime Pro Edition Software.