Is your run covered only to keep your chickens in? Or to keep flying predators out?
What I would do is start training your "wild" chickens. Spend more time around them. Go in their coop as its getting dark and talk to them, touching them briefly. When you feel them tense, take your hand off and move to the next one. After not terribly long, if you're consistent, you'll be able to leave your hand on longer and longer. Even if it is only a few seconds, progress is progress.
Also, I doubt they will run away. They know where their food and water is. They are creatures of habit and like to sleep in the same spot. If you start opening the door to their run about 15 minutes before they generally head to roost, they may come out for a peek and to scratch around a bit but will most likely go home to roost. Keep doing this, then start doing it 30 minutes before roost. Expand the time out of the run and the time your hand is on their back and I think you'll be pleased with the result.