Normally, JabRef migrates the preferences from a previous installation to the new version. Moreover, there shouldn’t be any problem when importing preferences from previous versions (maybe some changed settings are not imported correctly, but in general it should work). I have no idea why you run into these issues.
Probably it is, however, more time-efficient to just configure 4.0 again to your liking instead of troubleshooting the import problem. I’m sorry for the inconvenience caused.
If do get some log messages (in the error console), then feel free to open a bug report at GitHub and we will see what we can do.