Tuning part-throttle on the dyno can be very taxing on the cooling system if there isn't enough airflow available for the radiator. A WOT pull takes 6-10 seconds. You can be holding a load at part-throttle for as long as you want, the dyno cooling fan(s) must absolutely be up for it. I don't know who Matt Shue is and I'm not saying anything about his work. Just brainstorming based on my own experience here.
Like I said, if your cooling system isn't holding a vacuum, there is definitely a leak somewhere. It is not a dyno operator issue, or at least not anymore. Check compression and leak-down if there's nothing obvious.