Is the site that you used this on an html site or a dynamic site like PHP? I can see some potential issues in a dynamic site since tags may appear on the page that are only used under certain conditions based on the server side code.
If this is a static site please post back with some more details about what specifically was in the site and if you did any modification to any of the code produced by the WA tools. I will use this info to look into this issue further to help determine what may be going on and if there is a way around it.