This one's got me going... I have one user, me, having a limited role account and tried to elevate the role from Editor to Administrator through the Site Admin account. The user admin panel shows Administrator as it should but when logging in as the blog Admin, the menu items are those of a lesser account; Editor or Author. No Appearance, Plugins menus at all and the Settings menu doesn't show the standard entries: General, Writing Reading, Discussion--only menu entries from a couple of plugins. Another user having an Administrator role does show the proper menus, so the cap system is working; just not for this one user. Even though the Site Admin and Blog Admin accounts are me, the emails are different, so I'm not seeing that there should be any connection between the two accounts, as far as WPMu knows; just in case there might be some security thing going on preventing an escalation of a user account to a higher role.