Jason, I think I have a similar issue.
Cart is on main domain. Client changed name of company, so I made an alias to a new domain. All links are to new domain.
Reinstalled a missing ssl cert yesterday for original domain. While in the aliased domain, the "not trusted" message shows up when it gets to ..... cart.php and checkout.php.
Is there something I can change to enter the original domain for the ssl cert on the cart.php and checkout.php pages?