I installed JabRef 5.0 from the .deb package on Ubuntu 16.04.

JabRef is not correctly associated with the .desktop file, so it doesn't show the icon in the launcher (it shows the default ?-icon instead).

The StartupWMclass in the .desktop file is org-jabref-JabRefMain whereas the application seems to use org.jabref.JabRefMain.

Changing the line in the .desktop file to StartupWMClass=org.jabref.JabRefMain resolves the issue.