Check if "Settings / Pages / Copy originals if needed" is ON.
FWIW, I tinkered with that quite a bit, and it didn't seem to matter, but I'll test it a bit more....
Edit: That may, indeed, be the key. If you choose Link to originals or Link to originals via scaled images, but don't check Copy originals if needed, you get an album in which the PDF is still in the correct place (the root of the output), but the link to it is pointing a level above that.
Try: (demo album removed)
But it's fiendishly difficult to test this because of browser caching. Even clearing the cache is sometimes not enough.
I had to manually upload the pdf files, they were not being uploaded, and once uploaded (as you noted) the links that pointed to the files were incorrect. I tried turning on copy originals if needed and uploaded again. The pdf files were then uploaded without me having to manually do it. After having cleared the cache and reloading the page it seems the issue is resolved. So the fix was changing the setting as you pointed out. Thank you Laza and jGromit. For your assistance in resolving my question.
"Settings / Pages / Copy originals if needed" TO = ON