It is probably an issue with people coming to your web site with http://www.yourdomain.com and then you returning them to http://yourdomain.com.
They will act as different sites and have different sessions so if you shop with one and return to the other the cart will be empty. The best solution is to use .htaccess to force people to always (or never) have www. in the url and make sure to return to the same version. Just google "htaccess force www" and you will see how it is done.