The following is happening on v3.90
Steps to recreate:
1) Setup some Checkout Attributes on the Checkout Page. In my case it is "Invoice Number". It is required.
2) AS A GUEST, add a product to your shopping cart.
3) On the Shopping Cart page, populate the Checkout Attribute (ex: Invoice Number) and the select "Continue Checkout"
4) On the Welcome screen, login as an existing user
5) When returned to the Shopping Cart page, notice that the Checkout Attribute (ex "Invoice Number") is erased.
The desired behavior is that checkout attributes persist after a user logs in or registers.