Sounds like you might have some duplicate files repositories set up. From the command line, the repository lists are in /etc/apt. The main file is sources.list, which on my device is empty. Other lists are in /etc/apt/sources.list.d/. I have only "hildon-application-manager.list in there, but it is possible to have multiple files. They will all be combined together when you run apt. So I'm saying you need to check the files under /etc/apt to see if you have any duplicate entries. Don't change these files without saving a copy!