The results of the simulink scope and linear analysis step response are different?

When I use Linear Analysis to see the step response of my model, I found it's different from the scope in my model. And it's a huge difference although they are both stable. It's a digital control three-loop servo system. The controllers are digital and the object is a PMSM and there are some unit delay blocks in my model. I found that the difference only shows after I added the unit delay blocks.