It might be a silly suggestion, but have you restarted the webserver after making the php.ini changes?
Another method you might try using is to append a file using the "auto_prepend_file" directive to include a script to tighten up the open_basedir directive to the current users directory:
From PHP.net (http://www.php.net/manual/en/ini.sect.safe-mode.php)
As of PHP 5.3.0 open_basedir can be tightened at run-time. This means that if open_basedir is set to /www/ in php.ini a script can tighten the configuration to /www/tmp/ at run-time with ini_set()
ADDITIONAL SUGGESTION:
The Apache configuration will need to be set up properly for INI overrides to be effective. Ensure that you have "AllowOverride Options" or "AllowOverride All" set in the Apache config for your Server or Virtual Host.
http://us2.php.net/configuration.changes
http://httpd.apache.org/docs/2.0/mod/core.html#allowoverride