The visitor generator plugin will always write it's data to idSite = 1 - even when the user selects a different site from the dropdown.
The input form uses both request variables and post variables - the request idSite is the current site ID that the superuser is set to view (which in my case is always 1 when i choose settings) whilst the idSite from the dropdown box is being passed as a post. When the controller goes to retrieve the dropdown variable it returns the value from the URL, not from the POST.
The fix is to rename the site dropdown box variable so it gets passed properly to the controller.
(In ) fixes #1727