Many people have experienced this very annoying bug that Adobe has created in Audition 3, and unfortunately they have made the necessary efforts to research and fix it. Someone at Adobe Forums said that they cannot reproduce the problem in their labs, but I don't understand how I can reproduce this problem in under 5 minutes as well as many other people.
The good news is there's a work-around for this problem until (if ever) Adobe decides to invest some time to fix it. You don't need to force Audition 3 to close via the Task Manager when this happens. All you need to do is bring the main Audition window in focus and execute a copy command using your keyboard (CTRL+C).
In order to bring the main window in focus click on the Audition button on the Windows taskbar. First, Audition will minimize. Then, click on the Audition taskbar button again to bring it back and this will cause the main Audition window to be in focus. You will notice the window title bar at the top will become blue (or whatever color your Windows theme uses) indicating that it is in focus. Since Audition won't respond to mouse clicks while in this "paralyzed" state, you'll have to do a copy command using your keyboard (press CRTL + C). This should restore functionality, however please note that the command or effect you were originally applying to the sound will have to be done again. For instance, if you were using the Equalizer and you clicked OK to apply the change and Audition freezes, that change won't happen at that time. So you'll just have to go back to the EQ and redo the effect. Luckily, Audition seems to respond to keyboard commands and somehow "snaps it out" of this state.
As a matter of fact, any command that causes a progress indicator to pop up momentarily should snap Audition out of this paralyzed state and restore its functionality. Someone at Adobe forums originally suggested to press CRTL+SHIFT+S which brings up the Save As box in order to restore Audition to normal operation, but I found that you have to actually save the file in order to restore functionality, which may not be what you want to do. If you click Cancel on the Save As box, Audition remains paralyzed. It is better to do a Copy command instead which is harmless, quicker and simpler. You can explore other keyboard shortcut commands if you want, and most of them should kick Audition back into normal behavior after it freezes like that.