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Has this issue been corrected or are hidden templates still causing issues with Pages module? See: http://ellislab.com/forums/viewthread/204426/. I have a site I am about to update that has about 100 entries and want to be sure first. Since they use Pages module in EE, we typically have made the templates hidden in the past to avoid double SEO entries. See this method that we have used in past: http://www.fatfreeinteractive.com/blog/post-title/expression-engine-pages-module-tutorial.
Bryan