Re: mouse focus issues seemingly related to nvidia binary module
What makes you think this is the graphics driver's fault? It sounds to me like something in your desktop environment is grabbing the mouse, or your X server and/or its input drivers are buggy. The only way this could be related to the graphics driver would be if the screen were completely frozen, but it sounds like you can still interact with the system with the keyboard.
Does the problem still occur if you remove vbox? I've seen a number of reports from people running vbox and experiencing bizarre system instability problems.