The problem is that the cookies can only be read by the domain that created them, so when you hit your checkout.html file you can not read the cookie if you are switching domains in the process.
The solution is to not rely on the cookie. If you notice, the variables you need are passed along via a GET method of the managecart.html. So what I have done is port the CheckoutCart() function from the nopcart.js file over to php
Copy the code below and save it as a plain text file with a file extension of php. Read the usage comments located in the top of the code.
I have tried to maintain the payments options, but have not tested them. I wrote this for a client that processes their own credit cards, so I use another script I wrote and posted called MyCheckout to store the information in a MySQL database.
Hope this helps someone else out with the problem I had. Good luck and Aloha.
*** EDIT 01.30.05 ***