When viewing the capabilities in a role, the permissions that role already has are not indicated by the presence of a filled tickbox. For example, the administrator role has 67 capabilities, but none of them are ticked when you view it's edit page.
Similarly, when creating a new role, you can tick however many capabilities you wish and it will accurately create that role with associated capabilities. But when attempting to view/edit those capabilities after creation, the chosen tickboxes will not be filled.
In effect, you can add more capabilities, but you cannot remove them.
Is the plugin supposed to work like this?
Clean install, no other plugins.