Mouse not interacting with the windows on ubuntu

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http://askubuntu.com – For some reason when navigating through the OS its like there's a mode that swtiches from moving the window to navigating through the things inside the window and I have no idea what is going on. I am brand new to Ubuntu and linux in general. If there is any help that any can give all will be much appreciated. I am using a R.A.T 5 mouse if that triggers anything. (HowTos)