You're not going to like my answer... Anyway - get rid of "3-d bars" and "raised" pie. These fancy features do not add any useful informtion, and only add to small but annoying problems like this one with PDF. And take memory and much more time printing. And much larger PDF files than with plain pie and flat bars.
Take a look at this post: http://community.qlik.com/message/136696#136696, especially the response from John W.