I have the exact same issue.
I am using the Marlin firmware on Ramps 1.4, on a Mendel type printer.
Simplify3d 3.0.2
And I have attached my settings:
As my picture show I experience the same problem every time I print. If I print more models, it is only the last model that has the problem, which confirms the "skipping rest of instructions" theory.
I have tried to print from SD card and directly though USB - Same result. Is this problem unique to Marlin/Sprinter firmware boards, or does anyone experience this on Ultimaker etc. as well?