Thanks to Milo I got some direction in debugging this. Basically only the post_type of ‘post’ was being used in the SQL query for the daily archive. We can hook into this with pre_get_posts (which I had used earlier by my function was too specific).
The function on this page, tells wordpress to include all post_types in its global $wp_query.
http://uncommoncontent.com/2010/10/12/custom-post-types-in-the-loop-using-pre_get_posts-refined
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