When I drag-n-drop PDF file into existing entry I noted that in the dialog box 'How would you link to link to /home/path/file.pdf ...' the File Directory is the same current file of the .bib file, although I set it as a './subdir' both in Preferences and Database Properties.
Seems to be fixed in the current development version. If not, please report back to us and we will open this bug again.