Thunderstorms commonly make dogs nervous. Have you tried a ThunderShirt? It's kind of like swaddling for dogs - the compression of the vest calms them. It might be worth a try. I have friends who say that they've helped their dogs.
I had a dog like that once and the vet told me to ignore the thunder and go about my business. In time the dog learned that the thunder was nothing special. However, my dog hadn't been abused or anything like that. I imagine it's tougher in those cases.