• I have tested the latest master version from http://builds.jabref.org/master/ and the problem persists

JabRef version 4.3.1 on Windows 10

Jabref generates an absolute path to file if the relative path would "climb" the directory tree

Steps to reproduce:
0. assume you have a file "C:\foo\file.pdf"

1. set file directory (whether main, general, or user-specific) to "C:\bar"
2. right click on any JabRef entry -> select "Attach file"
3. navigate to and select "C:\foo\file.pdf"
4. The path to file will be stored in absolute format "C:\foo\file.pdf" instead of relative "..\foo\file"

Note that JabRef (at least on Windows) still handles correctly relative paths which include ".." (or start with "\") as long as you type them yourselves.