Probably because the output settings in the Model Initialization file are different. These can be accesed in the NEiEditor. On you could be using different contour plot options. Be sure you are comparing the same thing - not element vs nodal stresses, element internal vs corner stresses, etc. An d don't just look at the contour plot output, rather look at individual element stresses.
What type of elemetns are you using? How are you making the comparisons? How much different are the stresses?