Hi,
I just tried one of the latest dev 4.0.0 versions and it works fine:
However, you have to use a special version in which all libraries are in an external folder and you then have to use the startup script.
Create it yoursefl:
You just need to clone the JabRef repo, and run ./gradlew build (ignore the failing tests). (To compile it, you temporarily need oracle JDK8 enabled)
It creates a tar and a zip file in \jabref\build\distributions
Extract the archive and in the \bin folder you have a Jabref.sh script. That works fine with java9.
I am using XUbuntu 16.04.2 LTS and started JabRef with the shell script and it works fine.
Java™ SE Runtime Environment (build 9-ea+158)
Java HotSpot™ 64-Bit Server VM (build 9-ea+158, mixed mode)