From the JMP Help:

"The option Show Normal 50% Contours shows areas that contain roughly 50% of the points for that group if the assumptions are correct. Under linear discriminant analysis, they are all the same size and shape."

My additions:

Assumptions: a normal distribution with common covariance for the two groups.

Remember that the ellipse is an ESTIMATE based on the model. It is not a guarantee of having 50% of the observations within the ellipse.

Dan Obermiller