Could it have anything to do with this warning message in the beginning of running innobackupex? :
[root@boat-db01 ~]# innobackupex --stream=xbstream /tmp --defaults-file=/etc/my.cnf | nc backup-boat-db 9666
InnoDB Backup Utility v1.5.1-xtrabackup; Copyright 2003, 2009 Innobase Oy
and Percona Inc 2009-2012. All Rights Reserved.
This software is published under
the GNU GENERAL PUBLIC LICENSE Version 2, June 1991.
120515 17:27:16 innobackupex: Starting mysql with options: --defaults-file='/etc/my.cnf' --unbuffered --
120515 17:27:16 innobackupex: Connected to database with mysql child process (pid=10144)
120515 17:27:22 innobackupex: Connection to database server closed
IMPORTANT: Please check that the backup run completes successfully.
At the end of a successful backup run innobackupex
prints "completed OK!".
innobackupex: Using mysql Ver 14.14 Distrib 5.1.55, for unknown-linux-gnu (x86_64) using readline 5.1
innobackupex: Using mysql server version Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights reserved.
innobackupex: Created backup directory /tmp
120515 17:27:22 innobackupex: Starting mysql with options: --defaults-file='/etc/my.cnf' --unbuffered --
120515 17:27:22 innobackupex: Connected to database with mysql child process (pid=10258)
120515 17:27:24 innobackupex: Connection to database server closed
120515 17:27:24 innobackupex: Starting ibbackup with command: xtrabackup --defaults-file="/etc/my.cnf" --backup --suspend-at-end --target-dir=/tmp --stream=xbstream
innobackupex: Waiting for ibbackup (pid=10300) to suspend
innobackupex: Suspend file '/tmp/xtrabackup_suspended'
xtrabackup version 2.0.0 for Percona Server 5.1.59 unknown-linux-gnu (x86_64) (revision id: 417)
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 = ibdata1:1000M:autoextend
xtrabackup: innodb_log_group_home_dir = ./
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 1073741824
xtrabackup: using O_DIRECT
120515 17:27:24 InnoDB: Warning: allocated tablespace 772, old maximum was 9
>> log scanned up to (13769977313464)
[01] Streaming ./ibdata1
>> log scanned up to (13769978544611)
>> log scanned up to (13769980201056)
>> log scanned up to (13769981458447)
>> log scanned up to (13769982853138)
>> log scanned up to (13769983888634)