SOLVED MY ISSUE!
Hi, I was having the same issue as O_Connor_Electric. Save as Adobe PDF was causing certain images to disapper from the saved PDF. I found what was causing the issue on my document so I thought I'd share.
My file had rogue blank Shapes and Text boxes that were causing the issue, once removed the Save as Adobe PDF worked fine. To find them I clicked on a picture, select Picture Format > Selection Pane. In my screenshot you can see the offending blank items. Deleting these fixed it. I had no idea they were there, so I assume they were accidentally created or pasted in. Hope this helps someone else!