That sounds like a strange one. Some recommendations...
1. From SQL Developer's main menu bar, try Window > Reset Windows To Factory Settings, or
2. Install the latest 4.0.2 patch release. You will have the option of migrating / not migrating your 4.0.1 user settings.
If (1) does not help, doing (2) into an empty folder has multiple benefits: install is clean; user settings "cleanest" (no migration) or "cleaner" (migration, but with possible exposure either to migrating corrupt settings from earlier version, or possibly migration bugs); and, getting latest code fixes.
Alternately, if you prefer to stay with 4.0.1, you can take the middle road and reset all your user settings. Just rename or delete these folders, then relaunch without user settings migration...
1. %APPDATA%\SQL Developer\system220.127.116.11.48
In fact, adjusted for the specific system<n.n.n.n.n> folder, this step is the "gold standard" for verifying user settings corruption is not the problem. It also helps ensure SQL Developer is not pointing to some older JDK still installed on the machine.
SQL Developer Team