Comment 1 for bug 664986

Tried with the latest 1.6:

~$ innobackupex --user=root /home/gval/
...snip...
xtrabackup Ver 1.6 Rev 245 for 5.1.55 unknown-linux-gnu (x86_64)
xtrabackup: uses posix_fadvise().
xtrabackup: cd to /var/lib/mysql
xtrabackup: Target instance is assumed as followings.
xtrabackup: innodb_data_home_dir = /
xtrabackup: innodb_data_file_path = var/lib/mysql/ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 5242880
110502 14:53:59 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
InnoDB: File name /var/lib/mysql/ibdata1
InnoDB: File operation call: 'open'.
InnoDB: Error in opening /var/lib/mysql/ibdata1
110502 14:53:59 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
xtrabackup: Could not open or create data files.
xtrabackup: If you tried to add new data files, and it failed here,
xtrabackup: you should now edit innodb_data_file_path in my.cnf back
xtrabackup: to what it was, and remove the new ibdata files InnoDB created
xtrabackup: in this failed attempt. InnoDB only wrote those files full of
xtrabackup: zeros, but did not yet use them in any way. But be careful: do not
xtrabackup: remove old data files which contain your precious data!
innobackupex: Error: ibbackup child process has died at /usr/bin/innobackupex line 342.
~$ echo $?
2

Can you please also try if you can reproduce the issue with XtraBackup 1.6?