The workflow is updating the field directly to the database and not through the UI. The onchange/JScript event only works when the form is open and the value changes on the field, this is a separate process from how the workflow is updating the field. The workflow is an asynchronous process that is not tied to the open form. Hopefully this makes sense to you, what exactly are you trying to accomplish? You may need to remove the logic from the workflow to a plugin.
Good Luck!