The main difference I saw is that the Prusa file was using 6000 mm/min (100 mm/s) for the infill, but you have S3D set to use 9000 mm/min (150 mm/s). I you want to compare the prints you should really be using the same speeds.
As you start moving faster, you usually have to increase the temperatures and potentially also the extrusion rate. Otherwise you will see the broken infill like in your photo. There's some other good suggestions here:
https://www.simplify3d.com/resources/pr ... ak-infill/