This could very well be the case.
I will have to check the code to be absolutely sure, but it sounds like its having issues with the superadmin being added in conf, but not actually being entered into the database. If this is the case, its in my opinion a bug and needs to be fixed.
Workaround is simple until then, ensure that superadmin's in conf are members first, or are given at least one entry in one of the admin groups trough the !admins command.