Bernese Mountain Dog that we rescued about a year and a half ago...help?

She was sooo shy when we first got her. She has come a long way but still has issues. She always sits up against a wall, under a table or behind the woodstove we have in the living room. I try and coax her out and keep her out cus it doesn't seem healthy. She is fearful of loud voices and will make a quick exit to her bed. She is ALWAYS on my heels and stares at me all the time and at times she will put her paw on my lap and be shaking all the while snuggling in and when I leave and come back....OMG! I love her to death but she is really wary of my husband...one minute she is coming for a cuddle next minute she acts like he just beat her. How can we get her past it? She has gone to Obedience School - helped a bit, we put her on treadmill nearly every day.... I try to not acknowledge the hyper activity when I get home. I don't know what to do wth her....Just want her to be normal and like Caeser says...."balanced" Has anyone had a shy dog like this and managed to bring them out of it?