Due to a limitation of the JAM programmer, if you have more than one device in the JTAG chain on the Intel® Stratix® 10 FPGA development board, programming with a JAM file may fail.
This is because there is an Intel MAX® 10 device on the development board which multiplexes the JTAG chain via the Virtual JTAG IP. This IP introduces extra padding bits to the IR and DR which results in the failure.
Ensure that only the Intel Stratix 10 device resides in the JTAG chain on the development kit when programming it with a JAM file.