I have a feeling that your Org-noter is doing what it is designed to do.
See this part of its README on GitHub.
In a document
Run M-xorg-noter
when viewing a document (eg. PDF, epub…).
This will try to find the respective notes file automatically. It will search in all parent folders and some specific folders set by you. Seeorg-noter-default-notes-file-names
andorg-noter-notes-search-path
for more information [my emphasis]
If you “associate” an org file with a PDF document with using the :note-document:
property within the org file, you would need to start org-noter
in it, not in the PDF document.