[eluser]Ajaxboy[/eluser]
I an unfamiliar with what you are doing in the posting above. The snippets you posted from the ajaxframework don't seem to be a problem, and if they are - Likely something is off on the php install.
If the issue was what you suggested AjaxFw would print the error "Controller not found" or something similar, or php would generate an error.
$controller will be empty if you don't specify a controller, $_SERVER['QUERY_STRING'] will also be empty if you are not passing a query string.
Could you post your custom code, or the code you are using to access the AjaxFw
Do you have an online testing demo?