you need something heartier to deter the flies from landing and laying eggs. I live the pellet dust in the winter, but in the spring/summer/fall the straw holds water and the pellet dust degrades too quickly.
Try the deep mulch method for your run. Use the larger pine shavings from the farm store, not the fine stuff. If you can get it 3 inches thick you will deter the flies. The shavings dry out the droppings and their fluffy nature doesn't hold the moisture. The flies don't like laying eggs in it.
The ONLY time I have had trouble with flies was when I Spring cleaned the run in preparation for new shavings, cleaned it down to dirt, and then went to the farm store for shavings and they were out. I went a week without shavings and only a dirt floor. WORSE case of flies ever! LOL. As soon as the shavings went down again, the flies were gone.