Does Multi Site add additional capabilites that the Members plugin cannot see?
I tried creating a Power User role which was a mirror of the Editor role but with the edit_theme_options capability. It seemed to work fine till I got reports of users being prompted with Access denied when trying to access /subsite/wp-admin/ or being bounced to the wp-admin for the root blog.
After much debugging I noticed that although my Power User role had all the same capabilities checked as the Editor role, on the Roles screen the Editor role was listed as having 34 Capabilities and my Power User role only has 26 Capabilities.
Are there additional capabilities then that Members could potentially expose?