Do you have a url where I can see the problem? Most likely the issue is that you are redirecting to a different domain. For instance you enter the site using yourdomain.com and it returns you to www.yourdomain.com or maybe it takes you to an https:// domain that doesn't match the original domain name.
If the domain name changes then the session is cleared and you get an empty cart message.
If you send me a url where I can reproduce the issue I can be more specific in my diagnosis since this is just a guess.