Key chords involving the Control (Ctrl) key stopped working for me in VirtualBox v. 3.1.6. In other words, the Control key was not getting sent on to the guest operating system. Consequently Ctrl+C, Ctrl+A, Ctrl+X, Ctrl+V, and so on, had no effect.

I was able to get the Control key to work again by selecting File / Preferences in VirtualBox, clicking the Input section, and changing the Host Key from Control to a different key (I chose F12).

The Host Key is displayed on the bottom right of your VirtualBox screen, as the rightmost icon: