I'm not sure where to start...could you share your JMP table? I don't know what the design structure looks like? A full factorial on how many factors and how many levels?
If you only run the factors at 2 levels, your prediction profiler (which is both a main effects plot AND the model from the data incorporated into it) will only be able to estimate linear relationships.
"All models are wrong, some are useful" G.E.P. Box