Potentially an issue with 3dCart's canonical URL feature?
I think there is potentially a bigger issue with your site / URL structure causing this maybe. Have you recently changed whether your website makes use of www / non www in the URL's? Instances of both versions are indexed in Google currently - did you enter the canonical URL in 3dCart with the www or without. And if you use Google Webmaster Tools, is this set to display URL's with or without the www?
There is currently a www redirect from non www to www however, so one would presume www is preferred - so just ensure any settings in 3dCart's admin panel that include your domain, are inserted with the www included.
Maybe on this page.
Hope this helps initially.