Homepage Pagination fails with custom permalinks

The pagination of the homepage fails with pretty permalinks enabled, but functions when disabled. The pagination throughout the remainder of the website works without issue whether permalinks are set to default, or custom.

I’ve disabled all plugins to no avail.

I was thinking the issue was being caused by the custom loop which is being added to the homepage via the Siteorigin page builder, but the fact that it functions properly with the default permalink settings leads me to believe otherwise.

mod_rewrite is enabled on the server. It is working on all of the categories regardless of the permalink settings and I’ve checked via PHPInfo.

The website is using itheme’s security plugin, but the issue persists with it disabled. I also confirmed that its rules were removed from the .htaccess file.

WordPress is adding the same rules to the .htaccess file as are listed under Basic WP on this page, and they are not changed when permalinks are set to any custom structure: https://codex.wordpress.org/htaccess

Thoughts? Ideas?