Why does the Quartus II programmer display a JTAG USERCODE of 0xFFFFFFFF when programming with a .jic file, even when I have defined a unique JTAG USERCODE in my FPGA design?

Description

The Quartus® II programmer will display a JTAG USERCODE of 0xFFFFFFFF when programming with a .jic file, since a .jic is used to program an EPCS device which does not have a JTAG USERCODE field. This requires the FPGA to be configured with a Serial Flash Loader (SFL) image, which has a default usercode of 0xFFFFFFF.

The .sof generated for your FPGA design will contain the USERCODE as specified in your design and this is preserved when the file is converted to a .jic. Hence your unique USERCODE (if specified) will be programmed into your FPGA when it configures from the EPCS device, rather than 0xFFFFFFFF.