I have a sub-domain (wildcard) multisite installation, with two sites, I will call them Site A and Site B.
Site A and Site B both share the same theme, that has custom posts types declared in functions.php. On Site A the custom post types work just fine.
On Site B, I can see the CPTs in the UI, and if I try to add a new post saved drafts or posts go to the Posts section, instead of the CPT. It is very strange.
I have tried adding the CPT as different users (all of which are SuperAdmins), checked my permalink settings, and checked the .htaccess code to verify it matches the recommended code: http://perishablepress.com/press/2010/07/07/htaccess-code-for-wordpress-multisite/
Any ideas, or suggestions?