Thanks Semil - The same duplicates are not showing in Google Webmaster Tools, for instance SEOMoz is showing 639 duplicate page content and 646 duplicate page titles. Webmaster tools is 88 and 37 respectively.
Looking into the numbers in SEOmoz again (and they've risen since the original post) there's a huge number which fall under the capitalisation discussed but also some which seem to register as HTTPS and HTTP.