Not that I'm a big fan of Jython, but including startup time in a benchmark is only useful for very short running command line tools. It says nothing about the speed of the JIT or the code that's being tested.
But I think next time I do this I'll increase the max runtime from 1 minute to 3. That will keep more of the slower programs in the benchmark, and make startup time count that much less. Without actually removing it, because that seems too artificial and contrived to me.