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Sounds like corrupted initialization files. Easiest way to address this is to delete the <jdev_home>\jdev\system[X.X.X] directory (depending on the version you are running the directory name might be 'system' else something like 'system9.0.3).
This will cause all your end user customization settings to be lost (e.g. editor preferences, etc.) but will result in JDeveloper reinitializing to its 'out of the box' settings the next time you run it. None of your workspaces, projects, etc. will be lost. But, they will not show in the Navigator the next time you start up, so you'll have to do File | Open... to get them back.
Alternatively, you could try selectively restoring the system directory by copying the files in <jdev_home>\jdev\multi\system over top of the systemX.X.X equivalents. Start with palette.xml and see if that works.
Thank you! I was having the same problem and copying the palette.xml file over fixed it for me.
Glad to have helped.