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If both connections are the same and have the same privileges, you should get the same results. So let's assume you connect to both SQL*Plus and SQL Developer using the same user/password for the same host:port:sid/service (or tns alias or other method). What could be different?
How about the login script? Check if you have set:
Tools -> Preferences -> Database -> Filename for connection startup scriptPerhaps that sets one or more roles for the APPS user so all privileges you expect are active for the SQL Developer connection.
SQL Developer Team