Hi Steve,
Okay, this sounds like something is wrong on the server side. If the options on the back-end does not save, or only save partially, it could mean, that the php max_input_vars directive is set to a very low initial number. Please check the php.ini file for the max_input_vars directive, and change it to 3000 – that will be more than sufficient to pass on the post variables.
The plugin has a detection mechanism to check this directive, but php may not neccesarily report the correct local value of the directives.
I tried to log-in to check the issue directly, and debug it if needed, but I can’t access the site back-end – I have tried the /wp-admin/ as well as the wp-login.php access points, but they are not allowed. Can you please send me the back-end url?