You should be using one of the nonnormal distributions if your data does not follow the normal distribution. It's hard to say the appropriate distribution without seeing your data. It sounds like perhaps the Lognormal distribution may work. You can find an example of this in the Object Scripting Index.
dt = Open( "$SAMPLE_DATA/Process Measurements.jmp" );
obj =
Process Capability(
Process Variables(
:Process 1 & Dist( Lognormal )
),
Individual Detail Reports( 1 )
);
obj << {(:Process 1 & Dist( Lognormal )) <<
Process Capability Analysis(
Compare Distributions( 1, <<Fit Lognormal )
)};