This is a link to the dog whisperers website. He addresses issues such as this. It all has to do with who is the pack leader in the house, and how to establish yourself as the leader.
Also everytime you took her out of the crate while she was barking just made matters worse. Once in timeout they should not be let out if the bad behavior is continuing.
http://www.dogchannel.com/experts/ce...aspx?WT.srch=1