I don't know what your server is doing, or if its something related to upload, but I get the following error when the X3 panel tries to load the panel/x3_settings.php
<p>You don't have permission to access /nubierocce/panel/x3_settings.php
on this server.</p>
<address>Apache/2.2.16 (Debian) Server at http://www.zanichelli.net Port 80</address>
Check permissions on the uploaded files, although Im not sure it is that. The only other explanation is if your server has some misconfiguration. This is a NORMAL php script, and we need to access it with AJAX from the X3 panel. Your server is preventing it.
When clicking SAVE: