dealing with your indexing issue first - depending on when you submitted depends how soon those pages may be indexed. I say "may" because a sitemap (yes answering another question) is just an indicator of "i have these pages" it does not mean they will be indexed - indeed unless you've a small website you will never have 100% indexation in my experience.
Spiders (search robots) index / visit a website / page via another link. They follow links to a page from around the web, or the site itself. The more links from around the web the quicker you will get indexed. (this explains why if you've 10,000 pages you won't ever get a link from other websites to them all and so they won't all get indexed). This means if you've a web page that gets a ton of links it will be indexed sooner than those with just 1 link - assuming all links are equal (which they aren't).
Spiders are not cyclic in their searching, it's very ad-hoc based on links in your site and other sites linking to you. A spider won't be sent to spider every page on your site - it will do a small amount at a time, this is likely why 44 pages are indexed and not more at this point.
A sitemap is (as i say) an indicator of pages in your site, the importance of them and when they were updated / created. it's not really a definitive structure - it's more of a reference guide. Think of it as you being the guide on a bus tour of a city, the search engine is your passenger you are pointing out places of interest and every so often it will see something it wan't to see and get off to look, but it may take many trips to get off at every stop.
Finally, Canonicals are a great way to clear up duplicate content issues. They aren't 100% successful but they do help - especially if you are using dynamic urls (such as paginating category pages).
hope that helps