I just noticed after two years - my sitemap on one of my sites has ZERO urls indexed as shown in google's webmaster tools. However, my site is indexed all over the place in the search results. Why did I even bother? I think I need some major tutoring on sitemaps! lol
The count in Webmaster Tools is per sitemap. It shows the number of URLs selected to be indexed form that particular sitemap. So if your site is already indexed by other means such as crawling or other sitemaps then a sitemap might show 0.
The location of the sitemap dictates what URLs can be put in it. In your case only URLs under /Sitemap/ are allowed so /index.php would be ignored.
Ohhhh. Okay, thank you for that important piece of information. I'm not sure how this even happened. So stupid of me!! So, sitemap goes in root of folder/directory of the pages you want linked - you can't just provide a url within the sitemap and have the google bot know what you are talking about..... How could I not know this???