I believe this issue is the same issue as raised in these threads:
- Issue with Customer ID Handling on Shop Site with New Customer Accounts - #3 by Raphael_Pare
- Logged-In Customer Details Not Available in Online Store Theme with New Customer Accounts Through the Customer Liquid Object
Currently sitting with Shopify to clarify, but it appears as if the logged in cookie is only stored in the storefront for a short period of time, after which time expires and the session is then only available on the Customer Account domain.