Could you try clearing your saved settings (renaming the originals and/or exporting the connections) and try again, listing the exact steps you take.
Thanks for the tip. What I actually ended up doing which seems to have done the trick is removing the system_cache directory under the SQL Developer Preferences ( ~/.sqldeveloper/system220.127.116.11.80/system_cache/ ). Now I'm not seeing the errors I was seeing before. I'm still poking around to see how things would work with Git version control.
So I presume when I migrated the settings from my previous EA 4 version, one of the things which got copied is this system_cache info. It seems like if this is something which can be regenerated correctly on the next SQL Developer restart, this information should not be included in the migration from a previous version's preferences/connections.