Solution:
I fixed my version of the issue. Howefully its the same for you. The cookie was being set, but it was also setting a specific folder for the cookie. The AJAX call was one directory up from where the cookie folder was specified. This cause the cookie to be changed each time, which also created a new user each time and of course reset the shopping cart.
My solution was to set the cookie path for WPSC_CUSTOMER_COOKIE in wpsc-constants.php. Change the definition of WPSC_CUSTOMER_COOKIE_PATH which happens around line 55.
define( 'WPSC_CUSTOMER_COOKIE_PATH', '/' );