Are you working with large datasets. Or maybe importing step/iges files? Is Large Assembly mode triggering On?
From the SolidWorks Help:
Dynamic highlight from graphics view Model faces, edges, and vertices are highlighted when you move the pointer over a sketch, model, or drawing. (This option is not available when Large Assembly Mode is on.)
When you upgraded to SW2013 did you update your graphics card driver?
also, are you using a 3D "mouse"? - sometime re-running the calibration on the mouse will clear this up.