Reseting the Protégé preferences may fix some problems that Protégé has during initialization or when it tries to display data.

Sometimes the Protégé preferences become invalid or corrupted and Protégé is no longer able to start up or display things correctly. In particular, on some occasions the default font get set to something that does not work or a particular look and feel does not work correctly with Protégé. Reseting the preferences will put things such as

back to their initial default state. Most of this state can be quickly restored by going to the File->Preferences menu.