Many Wandora tools don't support parallel execution. You can't execute such tool while another instance of the tool is running. Wandora uses special locks to mark tools that are under execution. Tool is locked while execution begins and released when execution ends. Unfortunately there are situations when tool ends exceptionally and the lock is never released. Wandora may end up refucing to execute the tool again as it thinks there is another instance running. One way to resolve the unwanted locks is to restart Wandora. Sometimes this is undesirable. To clear all tool locks without restarting Wandora you can select Tools > Clear tools locks. Wandora gives you a popup informing the number of tool locks and releases all tools.
You should also beware. Wandora does not kill the thread that is running the tool. Wandora just allows you to rerun the tool. This means that releasing the lock does not automatically guarantee the tool can be safely executed again. This also opens up a chance to misuse the Clear tool locks feature by consciously executing the tool again while it is already running. Such misuse causes very likely Java exceptions or even worse, errors to your topic map.