I use screen a lot but found that the mouse scroll wheel would scroll the shell history rather than the window. This only happened in screen. Now I just had to remember this and thought I'd share the fix. The issue is in gnome-terminal (or Terminal as it's known in Ubuntu).
Simply right click in the Terminal and select Profiles->Profile Preferences. In the resulting window go to the Scrolling tab and make sure that Use keystrokes to scroll on alternate screen is NOT checked.