there's an issue about that : http://issues.ez.no/12621
currently there are two ways to fix this :
use the index_ajax.php script for ezjscore or ezcore extensions with some custom rewrite rules on URLs used in your call AJAX
if you wrote your own module/view for your AJAX calls, set the ui_context of your view to 'edit' or 'administration' or 'browse' or 'authentication' (see index.php around line 917)