Currently (in 10.1), pie charts seem to sit on top of everything regardless of the order of their layer in the table of contents. Make it so that the pie charts respect their order in the layering scheme of the map.
In my case, I have a layer with pie chart symbology sitting below a layer with mapped locations. For some region, the pie charts are on top of and obscuring the mapped locations. Actually, I can see that the pie charts are on top of the boundary of a layer four levels above (and also on top of all intervening layers).