I had similar issues when working with code that used DB-links to execute remote code and that remote DB raised exceptions that were not handled by "local" code (leaving distributed transaction open). In case of some exception types PL/SQL Developer did not retrieve DBMS_OUTPUT data (I had to execute some other code, eg. "begin null; end;" in that same window to make it retrieve what was left in the DBMS_PUTPUT buffer).
I can't specify the exact exception types that caused this behaviour as I did not make any notes and can't reproduce the behaviour now. I'm also not sure if the problem occured only in Test Window (I think it was SQL Window too).