You say she has the run of the house, but does she have somewhere 'safe' to run to? I am thinking of an indoor kennel/cage with a blanket over the top to make it like a den, leave the door open all the time. Sometimes dogs feel safer in smaller areas rather than in a big empty room/house.
It is very difficult to train for something that happens when you are not there.
I had a GSD that was absolutely terrified of fireworks and thunder, she would be trying to dig her way out of a concrete floor - and that was when we were in the room with her (plus my other two dogs were asleep, snoring!), there was just no way of getting through to her. Unfortunately she was like that all her life. I never found anything that could stop her going into total panic mode. The one time we had a thunder storm when I was out she actually broke one of her big back teeth trying to chew through metal mesh (put in the doorway to seperate her from her sister).
What is she like when you are home and there is thunder?