Here is the problem I am currently looking at.
The problem is happening when an item is being copied as a link to a site with a greater site id than the originating site. The listing of items then populate and Auto Index. When nothing is copied, the item I am testing against looks fine. This is because the item has not been pasted as a link yet. Also, note that The url is being generated via the $sys.assemblyItem variable.
Next, I paste the item as a link to a site where the site id is greater than the originating site. When using the same template to preview with the same Auto Index, I am now seeing that the site (and folder) of the pasted as link location are now displaying. I have set the mayHaveCrossSiteLinks variable set to true, and it did nothing.
I also just did a quick test out of box and didn’t replicate the problem the client is having.
Any help on what potentially could be the problem would be greatly appreciated.