A bit of a long-winded title, but if you reset any custom user permissions, changing the (global) moderators permissions afterwards doesn't set the permissions back. To recreate the problem, click on User Permissions, select a Global Moderator and reset all permissions to Not Set (No). Then click on Moderators,select the same user and change some of the permissions. Check User Permissions again and everything is still Not Set (No). You have to delete and recreate the global moderator to get the custom user permissions to stick again.