I reported a week or so again that I was having problems with the renders created by the pdf versions of my Sibelius 7 files. I ended up exporting them in individual pages as EPS files, then using Apple Preview to create pdf pages:
As you can see here, I had to uncheck “Use smallest bounding box” or the titles were cut off. Still, I had the hidden items, like the title for second through last pages, which appears as a gray object on the first page. So I went to the View tab and unchecked “Hidden Objects.”
That did the trick. I still had to combine the pages, using Acrobat, but the result was significantly cleaner-looking. I’m sure there is some kind of trick outside of Sibelius to do this as a batch, but I haven’t had time to hunt for one.