Shou..
I find if you position yourself on the Swiss ball so your upper body is hanging off the ball a little lower then ball height and then come up but only partially to retain tension on your abs and then go back down a little lower then ball height you will really start to feel it after about 15-20 reps. Do them at a controlled pace as well not too fast and remember not to come up too far or you lose tension on the abs and won't get as much of a punch from the crunches.. doing that really works for me..
You know you came up too far when you suddenly feel the pain/tension go away just about so gauge it that way..
Also try and keep your feet and knees closer together if not completely, it places more stress on the abs as you try and balance yourself more..
Swiss ball crunches are quite a bit harder to do effectively then most people realize..