Also having this problem. @Vladimir – have sent the details via the contact form because I forgot to check the forum.
Replicate: Network Admin > Users > User Role Editor > duplicate Administrator role > click Plugins in right hand menu to open “Allow manage plugins”, click Update button in the modal (make selections or don’t, it doesn’t make a difference) > all capabilities are wiped for the role.
Note that you don’t have to click the main Update or Update Network button to see this bug, the Update button in the “Allow manage plugins” wipes the capabilites and saves the role (refreshing the page or switching between roles demonstrates that).
