Fortunately there was a way to fix it! The latest version (1.4.0 at the time of writing) from the download page fixed the problem.
The latest DMG download also had the same error on launch as my original version, but the TAR download was ok. After doing some reading on the issue it looked to be a problem with JD-GUI needing to be recompiled on the latest Xcode.
I expect the real issue was with Launch4J needing to be updated to work with the latest macOS. Anyway after installing the new version it worked perfectly.