I have a trifold I've made and while exporting for my printer, I lose the drop shadows on the inside page (page 2). There are fewer drops shadows on the first page, and that side prints properly. The only difference between the two pages aside from the amount of drop shadows; is that most drop shadows are jpgs on page 2, and the outside page has only basic shapes. These same shapes show up on page 2 as well, but doesn't have drop shadows (therefore ruling out that it's because I have jpgs). I have to export it as a PDF 1.3 (Adobe 4) because that's what my printer specified with me, hence the only reason I'm running into transparency issues such as this. I'm running CS6 with Adobe Acrobat X Pro.
What do you mean when you say the dropshadows are jpg?
The objects that have drop shadows on page 2 are mostly jpgs, sorry for the confusion.