If you switch on log4j.logger.org.alfresco.web.scripts=DEBUG in log4j.properties, the Web Script framework will log where it's finding Web Script files.
Also, if you go to the Web Script index page /alfresco/service/ and locate your Web Script (or File Upload, if you're extending it), and click on its ID, it should dump the complete Web Script to the browser allowing you to see where all its implementation files have been picked up from.
Also, note, that the extensions/templates/webscripts folder must exist before starting the server. If it's not there at startup, it doesn't ever bother to look there, until a restart.