I did an install on the subdomain and the problem was still happening. Thought I’d follow up because I did manage to find a solution on my own. The index.php was being added in the url under Settings –> Permalinks –> Custom Structure. I just removed the index.php and it works under both subdomain and subfolder.
But the problem with the results being displayed by chapters instead of by books is a major sticking point, and I hope that is a priority in the updates soon. It’s really close to being a perfect solution to adding original works on the site