I have similar issues with .epub to .pdf conversion, actually.
The margins (set all four to 72) work. But they also work for the cover image which looks a little ugly now, since it doesn't stretch across the entire page anymore; instead, it's shrunk into the text box of the remainder of the book.
My .epub contains internal links for the TOC or footnotes. The .pdf shows these links in blue, but essentially not functional. Is something broken here? If there is support for internal links, then they don't work; if there is no support for internal links, then they shouldn't show up in blue. Either way, something seems broken.