If you are getting all of the items details into the db then it indicates the cart is being repopulated properly. If you are getting a message about the cart being empty then there is likely a problem with the email friendly cart display code that you are using. Rather than copy this code from another page you should go into the body tab of your Universal Email page and using the edit with DW button create a new cart display using the email friendly cart display. You can add in your logo back to the top of the page also.
I think this might fix the problem for you and get you the entire cart contents to display in the email. If you have any more problems with this let us know.