I wonder (I actually am not sure) if the issue is an Apple or Pages one. From my experiences in printing, I've found certain programs write better and cleaner PDF's than others. In-Design, for instance, exports PDF's in magnificent form, while a similar program, Quark Xpress, seems to fail in that department. Yet, assuming both are from the same Mac, using the same options, and same engine, why would one be better than the other?
Maybe this is like asking the meaning of life????