WPSEO / WooCommerce Breaks POSTNAME Permalinks When New Site Created (Multisite)

Setup

• WP Multisite – 4.1.1
• .htaccess and wpconfig.php are set to WordPress defaults
• Twenty Fifteen Theme
• Permalink Settings – Post name /%postname%/
• All Plugins (Network and Site specific) Disabled – EXCEPT WordPress SEO.
• WordPress SEO v1.7.4 – network activated
• WooCommerce v2.3.7 – activated only on top level site
• WooCommerce installed and pages setup (but does not have to be active) – for the test below I have deactivated WooCommerce, but it’s still installed and set up.
• The key point is that WooCommerce only needs to be installed and set up. It does not need to be active to reproduce this error.

Steps to Reproduce

1. View a post from the top level site – permalink is correct and post is displayed
2. Create a new site – WP network admin.
3. Refresh post from step 1 – 404 error, permalink broken
4. Go to Settings->Permalinks in the top level site and save permalinks
5. Refresh post from step 1 – permalink is correct and post is displayed

When a new site is created it breaks the post level permalinks only on the top level site – in most permalink configurations but not all:

• Default – Works as expected
• Day & Name – Works as expected
• Month & Name – 404 until I save permalinks
• Numeric – 404 until I save permalinks
• Post Name – 404 until I save permalinks – this is the one we use.
• Custom – 404 until I save permalinks

If WordPress SEO is then deactivated and the test is done again, all permalink configurations work as expected.

This is starting to look like a clash between WordPress SEO and simply having WooCommerce installed?

WooCommerce does create custom post types and categories which show on the permalinks page, so maybe a custom post type or custom taxonomy issue?
https://wordpress.org/plugins/wordpress-seo/