This only happens with the bundle DerbyPersistenceManager.
In DerbyPersistenceManager.close() the embedded derby database is shut down and then super.close() is called. There the ConnectionRecoveryManager is closed, which tries to operate on a connection to the already shut down derby database. The log contains entries like:
25.03.2008 13:49:29 ERROR [Thread-5] ConnectionRecoveryManager: failed to close connection, reason: No current connection., state/code: 08003/40000 (ConnectionRecoveryManager.java, line 453)