@Mark_Bailey explains discrepancy in this previous thread.
"The discrepancy measure is a relative measure of the quality of a space filling design solution. It is useful when comparing two or more space filling designs. A smaller discrepancy indicates a better design.
Discrepancy is the difference between the design points (which have an empirical uniform distribution) and a theoretical uniform distribution."
I am not sure which discrepancy measure this corresponds to in the R package. The documentation for the R package does not have a lot of detail.
Perhaps you might want to generate a space-filling design in JMP and then run it through diagnostics in the R package to see which measure is the same. Alternatively you might want to contact technical support to see if they can get more statistical details (support@jmp.com).
I hope that helps,
Phil