Well, it stands to reason that something must've changed is order to cause such a huge increase. Looking through the list of duplicate URLs, I'm seeing a lot that could be fixed by rel="canonical". There's enough of them that adding a canonical link to each would be a huge undertaking or require some careful coding. I'm wondering if this increase could've been partially caused by someone removing rel="canonical" from a lot of pages.
For example, I'm seeing a lot of this:
http://www.health2000.co.nz/shop/aromatherapy/lemongrass-essential-oil/P4494/C56
vs.
http://www.health2000.co.nz/shop/aromatherapy/lemongrass-essential-oil/p4494/c56
The only difference between those URLs is capitalization. The first, capitalized version is the one that appears on your XML sitemap. I'm not 100% sure why both versions would be appearing to Roger—it may be an issue with the CMS—but a rel="canonical" on the former pointing to the latter would solve that problem.
Now, that doesn't look to be the only issue, but it _is _a large one.
Let me know what you find out!