Post Indexer adding /blog/ to indexed permalinks of sub sites


I have a subfolder based Multisite install.

The permalinks for the subsites are set to /%postname%/ the permalinks on the main site are set to /blog/%postname%/

As an example, on a subsite the url of a custom post is:

That URL is working perfectly with no 404 errors.

Post indexer is set to index this custom post type across the network and is indexing all of the sites, however the URLs in post indexer all look like this:

Which is incorrect and throws a 404 error.

This makes the Global Site search and Global recent posts widgets useless.

I have enabled support access for the site.

I appreciate your help with this.