Joe,
I had the same problem and this was the reply from the 3DCart support:
"We don't fix errors in your webmaster tools account for you, this is a third party service that is not part of 3dcart.
We provided a free sitemap with your account, if it's not working as expected, you don't have to use it."
Anyway, this is the solution:
Go to settings>>general>>store settings, scroll down and change you store url to include
http://www.yourdomain.com
then go to settings>>general>>store modules and scroll down and hit "update file names" and save.
go to your ftp and find the folder "web", inside the folder find file "sitemap_cache.txt" and delet it
open any brobser and type
www.yourdomain.com/sitemap.xml and your new sitemap will be created.
then go to your webmasters tools and delete your site url, then input your site back using
www.yourdomain.com, include a sitemap:
www.yourdomain.com/sitemap.xml submit and everything will be fine.
As per the support, what can I tell you...almost all of them are great like in any place, sometimes they forget that nothing is for free and they have a job because we pay for their salaries...