This will happen if you shut down the broker process (bkrd or bkrd.exe) but do not shut down the rtserver process (rtserver or rtserver.exe).
On Windows, check the Processes tab in Task Manager. Look for any remaining Harvest-related processes (rtserver.exe, hserver.exe, bkrd.exe, agntd.exe) and kill those.
On Linux and Unix, execute "ps -ef | grep <process name>" to look for any remaining Harvest-related processes (rtserver, hserver, bkrd, agntd). Kill any remaining processes that you find.
Be sure to search for and kill the rtserver process as a last step. If you kill the rtserver process while the broker is still running, the broker will try to initiate a new rtserver process.
CA Harvest SCM all versions and platforms