I had this strangest problem with my mouse on Ubuntu. When using the left mouse button in a window, for instance Thunderbird, it was grabbing and moving the whole window rather than selecting things within the window. If I pressed the thumb button on the side of the mouse and the left button at the same time, the mouse performed as I would have expected the left button to do alone. Moreover, if I pressed “alt” and the left button it also worked propperly.
I do not know what the problem was but I know what I did to solve it. I went to “System->Preferences->Windows” in the menu in Ubuntu. In the “Windos Preferences” I reselected “alt” as the “movement key” and everything was back to normal. Apparently I must have reset some of the configuration options for the mouse/keyboard when reselecting “alt” as the movement key. As my knowledege about Xorg (the window system in Ubuntu) is limited I am glad I was able to fix it without any further configuration.