About a month ago, we made a new role based on the Editor role, added the manage_options capability, then "Applied to all sites." Now users with that Role can no longer manage options.
This is on a multisite installation. To test: All plugins have been turned off, except for URE, both on network and single site.
When attempting to Manage Options (Settings > General) and even Manage Theme Options (edit_theme_options also checked), we get the message, "You do not have sufficient permissions to access this page."
Users with that Role, previously, were able to do the above.
Here's a screencapture of the capabilities: