[cflsystems]

Well the auto generate works only on products without clean urls so if your products have clean urls assign to them already auto generate won't change anything.
Open skin1/check_clean_url.js and find

to_field.value = from_field.value.replace(/[\&]/g, '-and-').replace(/[^a-zA-Z0-9._-]/g, '-').replace(/[-]+/g, '-').replace(/-$/, '');

and after add

to_field.value = to_field.value.toLowerCase();

Now when you add new product in admin and enter product name and then move out of that field the url will be lower cases