I have the bootstrap index.php file that will load a default pages file for the non invisionboard directory. The directory itself will no longer load a default module, it will also load the default pages page. E.G. domain.com/ and domain.com/invisiondirectory both load the default pages page. Anyone else run into this? It was working fine in 4.1.13. Thanks.

Yes I had this. Check that your htaccess files are still in place and correctly named, particularly the one in domain.com/invisiondirectory 

Everything appears to be correct. When I change the default module under System -> Applications, it does not appear to update the friendly URL associated with the default suite installation directory. In my case /web/. I submitted a ticket.