Why is my 85 lb dog so afraid of everything

I have a half rotty/half german shephard female dog who is almost 2 years old. I bought her from a shelter when she was about 7 weeks old. It was a shelter who found pregnant dogs and helped them give birth to the puppies, and then try to find homes for them. So I'm pretty positive she was never abused.

She is 85lbs and pretty much afraid of everything: loud voices, popping sounds, anything falling on her, the shower, my big blue ab ball, any sort of plastic bag (you get the picture). She always runs away with her tail between her legs. However, when she is with other dogs, she is much more adventurous and I don't understand the sudden change. She did have puppy training and then the next level after it. Any ideas what I can do to rid her of this ridiculous skittish nature? I try to tell her its unbecomming of such a large dog, but she doesnt seem to listen to me! Any help is welcomed.

first of all, take a look at the video at the top of this page> http://video.google.com/videosearch?clie...

Rookie was a terrified dog..just born a very timid dog..When he was spoken to, he would roll on his back and pee all over himself..Carolyn discovered a training method that gave him a huge confidence boost, and now just look at him!

this method is so easy and fun that children love to do it> http://www.clickerlessons.com/

If you want to look at the other videos, all the dogs were trained by that method..On about the 5th page, two children show what they have done with their dogs..Wow!