I tested several times - With Eclipse+sqlexplorer plugin I connect to JavaDB using embedded driver (from JDK 1.6.27) using derby.jar (new profile had to be created). Once connected I disconnect. That works fine. I go to SQLExplorer app (with eclipse built in) and try to connect but I get exception saying that there is someone else already connected. However, if I close the eclipse+plugin I can connect with SQLExplorer app. That means the connection was not released until I closed eclipse+plugin
Note that JavaDB embedded allows only one connection to DB.