The site: command for Sootle is looking very clean. 275 pages indexed, with the Sitemap showing 270.
All the pages have clear descriptions and title tags. Thank goodness there is no suffering from the unsightly URL only problem you see with so many directories. I’m convinced that you need to exclude all dynamic crawling in Google if you use mod_rewrite. The number of sites hit by duplicate content filters should be a good indicator of how much that advice is needed.