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You could try minimising or moving some other panes to make the top of the dbms_output pane visible.
Failing that, you could delete windowinglayout.xml which will reset the windows to the defaults.
The file should be in SQL Developer\system3.2.20.09.87\o.ide.188.8.131.52.37.59.48 in your home directory (.sqldeveloper if not on windows
Thanks a lot Jim!