Duplicator don't copy all files

Same problem with max_execution_time as 360 seconds.
There are not disk quota problem.
The only red config option is on System Check screen :
Open Base Dir: On Fail (sorry: what is the “Open Base Dir” ?)
The only missing folders are “themes” and “plugins” and are not excluded by filter.
It is a strange behaviour, any help ?

This is the log :

********************************************************************************
PACKAGE-LOG: 03:01:28
********************************************************************************
duplicator: 0.4.3
wordpress: 3.5.1
php: 5.3.3
php sapi: cgi-fcgi
server: Apache
browser: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:20.0) Gecko/20100101 Firefox/20.0
package name: 20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy
php_max_time: from=360 to=5000
php_max_memory: from=128M to=5000M
mysql wait_timeout:5000
********************************************************************************
SQL SCRIPT
********************************************************************************
wp_commentmeta (2)
wp_comments (1)
wp_duplicator (0)
wp_icl_content_status (0)
wp_icl_core_status (0)
wp_icl_flags (63)
wp_icl_languages (63)
wp_icl_languages_translations (3969)
wp_icl_locale_map (2)
wp_icl_message_status (0)
wp_icl_node (0)
wp_icl_reminders (0)
wp_icl_string_positions (0)
wp_icl_string_status (0)
wp_icl_string_translations (0)
wp_icl_strings (0)
wp_icl_translate (175)
wp_icl_translate_job (18)
wp_icl_translation_status (5)
wp_icl_translations (124)
wp_links (0)
wp_options (397)
wp_postmeta (863)
wp_posts (123)
wp_term_relationships (86)
wp_term_taxonomy (18)
wp_terms (18)
wp_usermeta (64)
wp_users (2)
wp_w3tc_cdn_queue (1)
SQL CREATED: /data/vhosts/xxxxxxxxxxxxx.it/httpdocs/wp-snapshots/517550c842efd1246_20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy_database.sql
SQL TOTAL RUNTIME: 0.1551 sec.
********************************************************************************
ZIP ARCHIVE:
********************************************************************************
ARCHIVE FOLDER: /data/vhosts/xxxxxxxxxxxxx.it/httpdocs
ARCHIVE FILE:   /data/vhosts/xxxxxxxxxxxxx.it/httpdocs/wp-snapshots/517550c842efd1246_20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy_package.zip
FILTER EXTENSIONS:  ''
FILTER DIRECTORIES: ''
----------------------------------------
ZIPARCHIVE OPENED
DATABASE.SQL ADDED TO ZIP: /data/vhosts/xxxxxxxxxxxxx.it/httpdocs/wp-snapshots/517550c842efd1246_20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy_database.sql
log:class.zip=>new open handle 5009
ARCHIVE INFO: ZipArchive Object
(
    [status] => 0
    [statusSys] => 0
    [numFiles] => 5849
    [filename] => /data/vhosts/xxxxxxxxxxxxx.it/httpdocs/wp-snapshots/517550c842efd1246_20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy_package.zip
    [comment] =>
)

CLOSE RETURNED: '1'
ZIP TOTAL RUNTIME: 7.6559 sec.
ZIP FILE SIZE: 31.04MB
RECORDED ARCHIVE ID: 3
********************************************************************************
FINALIZATION ROUTINES:
********************************************************************************
BUILDING INSTALLER FILE
INSTALLER FILE BUILT
MAKING INSTALLER FILE
INSTALLER MADE: /data/vhosts/xxxxxxxxxxxxx.it/httpdocs/wp-snapshots/517550c842efd1246_20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy_installer.php
INSTALLER FILE COMPLETED
COMPLETE PACKAGE RUNTIME: 7.8249 sec.
********************************************************************************
DONE PROCESSING => 20130422_xxxxxxxxxxxxxyyyyyyyyyyyyyyyy 03:01:36
********************************************************************************

Hi c.barca,

Here is a helpful section on the FAQs page:
-> Browse To: https://lifeinthegrid.com/duplicator-faq/
-> Find Section: “1. Package”
-> See Question: “What is an Open Base Dir error or “open_basedir restriction in effect”?”

Hope that helps!