It could also be an issue with the processing that MS does. Have you tried to print to the Adobe PDF printer? You do not have the links in that case, but the result is sometimes different and might help give some idea of what the problem is.
Thank you for your response. You could be correct. It could be a Word problem with the Save as Adobe PDF option.
I tried the Save As option and selected the PDF Save as type, and it does work. (I selected the option to Create bookmarks using Headings, and that works great fortunately).
I have narrowed the problem to a simple test case, that you can try.
Create a new blank document in Word 2010.
Insert a header and a footer. (I chose the Austere).
Put a heading on the page. (I used the Heading 1 and typed This is a heading.)
Insert a line shape. (Insert | Shapes | select a line and draw a line).
Paste in a small image. (I did an Alt-Prnt screen of a small window, and then did a Ctrl+V to paste it into the Word document).
Move the line so that it is partly on and partly off the image.
Save the document.
Save it using the Save as Adobe PDF option.
It will open Adobe Reader or Acrobat and it will look correct. The line will be above the image.
Close the PDF file.
Back in Word, right-click on the image and select the Wrap Text | Behind Text option.
Save the document again.
Save it using Save as Adobe PDF again.
It will open Adobe Reader or Acrobat and it will not be correct. The line will be below the image.
So I think this points to the Save as Adobe PDF option as the problem.
I will try this if I can get WORD 2010 installed. I had tried before after I botched something and now OFFICE 2010 is giving me an install error on a machine that I was trying to put it on. If I get a chance, I will try to do it (but may not get to it for a week or so -- give me a ping if you want to remind me). That is an installation on Win8. Unfortunately, the Win8 install wiped out the prerelease version of Win8 that had been installed and all related programs. That is where I blew it.I will also have to read your post carefully to get to your point.
Maybe someone else will get a chance to try it in the meantime.