I've a similar problem... I don't necessarily disable open_basedir at all, but my error.logs will explode soon...
QuotePHP message: PHP Warning: is_readable(): open_basedir restriction in effect. File(/usr/share/pear/ZendX/Application/Resource/Db.php) is not within the allowed path(s): (/var/www/virtual/xyz/:/var/www/virtual/xyz/phptmp/:/usr/share/php:/usr/share/pear/:/var/www/virtual/xyz/:/usr/share/pear/:/tmp)
As you see, the error is some kind of confusing. For me, /usr/share/pear/... is absolutely within the given basedirs... or do I have been mistaken by the seperator etc.?