Yeah. I guess "not charging" means "not charging at the full speed you may expect." I get the same message using the ports on the front and the back of my HP desktop, whether I plug the cord directly to the iPad or plug the cord into the dock and put the iPad into the dock. In all cases, it does charge, a bit slowly.
Actually, iPad charging in general seems a little slow, but that's probably because the battery capacity is larger compared with most portable electronics.