Hi i've the same issue.
I've created a custom post type, and i've a single-custom_post_type.php and a archive-custom_post_type.php.
The archive-custom_post_type.php is a custom template, so i have created a blank page with that template for display my custom_post_type posts.
When i click to the permalink to the single post it works (wordpress load the single-custom_post_type.php) but in my breadcrumbs i've Home->Blog->custom_post_title, the correct structure is Home->custom_post_type->custom_post_title.
How can i do?
Thank you