URGENT switching to multisite killed Custom Posts types

Major bug and/or design flaw... switching a site to multisite mode automatically disables the CustomPress post type.

While I have found the checkbox in the network CP settings which has returned all of our custom posts to the dashboard and site, ALL of the links throughout the site are wrong -- our category base "blog" is being injected in front of all links.

Should be:

The word "blog" is our category base set in permalinks. "Modules" is our custom post type.

I have tried four permalinks resets and it never works. How do I get this slug out of our links?