Private files and javascript

I have private files turned on, looking at the source code i get this:

<script type="text/javascript" src="/misc/drupal.js?d"></script>
<script type="text/javascript" src="//var/www/virtual/example.com/example_files/languages/it_89e93bbcb5d0bdeae8ad9f15e3183339.js?d"></script>
<script type="text/javascript" defer="defer" src="/sites/all/modules/admin_menu/admin_menu.js?d"></script>

<script type="text/javascript">
<!--//--><![CDATA[//><!--
jQuery.extend(Drupal.settings, { "basePath": "/", "admin_menu": { "margin_top": 1 }, "googleanalytics": { "trackOutgoing": 1, "trackMailto": 1, "trackDownload": 1, "trackDownloadExtensions": "7z|aac|avi|csv|doc|exe|flv|gif|gz|jpe?g|js|mp(3|4|e?g)|mov|pdf|phps|png|ppt|rar|sit|tar|torrent|txt|wma|wmv|xls|xml|zip" }, "lightbox2": { "rtl": "0", "file_path": "/(\\w\\w/)/var/www/virtual/example.com/example_files", "default_image": "/sites/all/modules/lightbox2/images/brokenimage.jpg", "border_size": "10", "font_color": "000", "box_color": "fff", "top_position": "", "overlay_opacity": "0.8", "overlay_color": "000", "disable_close_click": 1, "resize_sequence": "0", "resize_speed": 400, "fade_in_speed": 400, "slide_down_speed": 600, "use_alt_layout": 0, "disable_resize": 1, "disable_zoom": 0, "force_show_nav": 0, "loop_items": 0, "node_link_text": "View Image Details", "node_link_target": 0, "image_count": "Image !current of !total", "video_count": "Video !current of !total", "page_count": "Page !current of !total", "lite_press_x_close": "press \x3ca href=\"#\" onclick=\"hideLightbox(); return FALSE;\"\x3e\x3ckbd\x3ex\x3c/kbd\x3e\x3c/a\x3e to close", "download_link_text": "Download Original", "enable_login": false, "enable_contact": false, "keys_close": "c x 27", "keys_previous": "p 37", "keys_next": "n 39", "keys_zoom": "z", "keys_play_pause": "32", "display_image_size": "", "image_node_sizes": "()", "trigger_lightbox_classes": "", "trigger_lightbox_group_classes": "", "trigger_slideshow_classes": "", "trigger_lightframe_classes": "", "trigger_lightframe_group_classes": "", "custom_class_handler": 0, "custom_trigger_classes": "", "disable_for_gallery_lists": true, "disable_for_acidfree_gallery_lists": true, "enable_acidfree_videos": true, "slideshow_interval": 5000, "slideshow_automatic_start": true, "slideshow_automatic_exit": true, "show_play_pause": true, "pause_on_next_click": false, "pause_on_previous_click": true, "loop_slides": false, "iframe_width": 600, "iframe_height": 400, "iframe_border": 1, "enable_video": 0 } });
//--><!]]>

</script>

If you look for example you'll find an internal path to files instead of something else.