I was able to determine that part of my problem was related to secured PDFs. With an unsecured PDF, the preview window does not render the markings (besides the page thumbnails as I described earlier) but you can see them on the PDF in the actual note. Edit: I discovered I did not have the latest version. If you have an App Store-installed version of Evernote, you are not running the latest version. The App store version is 5.4.1 at this time and the latest is 5.4.2, in which this issue was fixed. Re-download Evernote from the evernote.com web site and that should fix the problem.