We are having difficulties with PDF files placed in our layouts. After transitioning from 12 to 13 we now find that PDF files that are placed in our project do not respect the original files they came from. Drawing manager shows them as missing, and an attempt to point them tot he appropriate source file only replaces them with a blank drawing. Before the PDF was missing, but the drawing info still showed (stored with file). We deleted the placed drawing and then manually placed the drawing again thinking it would generate a new link. But it still wont recognize the PDF.
Ultimately, we had to rename the PDF in the finder before successfully placing it again. Now the link is respected.
We experience this problem too, especially with images and still haven't managed to cure it.
Relative/Absolute makes no difference and I suspect it's not even a factor, although AC probably checks the drawings status (especially when Drawing Manager is open) and it's during that process that I think it falls over. Not sure why though.