I enabled multisite on an existing WordPress install (3.5.1 with genesis 1.9.1). Links to custom post type posts were working before I enabled MulitSite. Everything with the MultiSite is working fine except a pre-existing custom post type is returning 404 errors. If I set 'rewrite' => false the posts load. But putting back the slug it doesn't.
I have tried switching 'with_front' between true and false and every other post I have stumbled across when searching for a solution and nothing seems to work.
I went to the permalinks page in the admin and saved before testing each change.
The url that is being returned by get_permalink() is.