Hello,
I'm sorry, but I can't tell for sure, it depends on why there are such duplicate URLs created. We would need to find the places where those URLs are created and with SEF completely disabled check their original non-SEF structure, to see why they're duplicated.
You can either do this by yourself and post some examples of non-SEF URLs for the duplicated SEF URLs, or you can purchase our paid support service and we can check this for you:
www.artio.net/e-shop/support-services/joomla-related-support-1h