Thank you for your quick reply Oleg. I have a link to these new folders from my index page. I must have a link to these new folders otherwise my site wouldn't work - there would be can't find errors - wouldn't there? I use dreamweaver to make my site - the link to the new folders are from a pop up but I wouldn't think this would be the problem. Does it just take time for Googlebot to find these new folders or should they instantly appear in the newly generated xml sitemap?
My site and all links are fine. It's just that the new folders are not in the site map.