matlab compiled as jar using mre is slow

I have some matlab code that is compiled into a jar. I install the matlab runtime environment and make calls to the jar and it works, but its extremely slow. Calls that takes seconds in normal matlab are taking minutes when I call the jar. I've evenly tried setting the thread that its running on to max priority but it just doesn't speed up. Any one know why this would be occurring, or what could cause this to happen?