xtrabackup seems to ignore innodb_data_home_dir on target

When I do a backup and specify the source mysql conf file and target conf file, it always ignores the innodb_data_home_dir parameter in the target configuration file.

Command: xtrabackup_55 /var/lib/mysql/backup/real.cnf /var/lib/mysql/backup/mb1.cnf --target-dir=/var/lib/mysql/backup/i1 --backup

##contents of /var/lib/mysql/backup/real.cnf
#-bash-4.1$ cat /var/lib/mysql/backup/real.cnf
datadir=/var/lib/mysql/i1/data
innodb_data_home_dir=/var/lib/mysql/i1/innodb/data

##contents of /var/lib/mysql/backup/mb1.cnf
#-bash-4.1$ cat /var/lib/mysql/backup/mb1.cnf
datadir=/var/lib/mysql/backup/i1/data
innodb_data_home_dir=/var/lib/mysql/backup/i1/innodb/data

output from backup below. Notice that it puts the ibdata1 file here “/var/lib/mysql/backup/i1/ibdata1” and not in the specified directory “/var/lib/mysql/backup/i1/innodb/data”

xtrabackup_55 version 1.9.1 for Percona Server 5.5.16 Linux (x86_64) (revision id: 398)
xtrabackup: uses posix_fadvise().
xtrabackup: cd to /var/lib/mysql/i1/data
xtrabackup: Target instance is assumed as followings.
xtrabackup: innodb_data_home_dir = /var/lib/mysql/i1/innodb/data
xtrabackup: innodb_data_file_path = ibdata1:10M:autoextend
xtrabackup: innodb_log_group_home_dir = /var/lib/mysql/i1/innodb/logs
xtrabackup: innodb_log_files_in_group = 2
xtrabackup: innodb_log_file_size = 268435456
120427 14:32:32 InnoDB: Using Linux native AIO
xtrabackup: using O_DIRECT
120427 14:32:32 InnoDB: Warning: allocated tablespace 49, old maximum was 9

log scanned up to (1433402778)
[01] Copying /var/lib/mysql/i1/innodb/data/ibdata1 to /var/lib/mysql/backup/i1/ibdata1
[01] …done
[01] Copying ./wmaint/BILL_SUPPLIER.ibd to /var/lib/mysql/backup/i1/./wmaint/BILL_SUPPLIER.ibd
[01] …done
[01] Copying ./wmaint/REQUISITIONSUMMARY.ibd to /var/lib/mysql/backup/i1/./wmaint/REQUISITIONSUMMARY.ibd
[01] …done
[01] Copying ./wmaint/ORGANIZATION.ibd to /var/lib/mysql/backup/i1/./wmaint/ORGANIZATION.ibd
[01] …done
[01] Copying ./wmaint/SUPPLIER.ibd to /var/lib/mysql/backup/i1/./wmaint/SUPPLIER.ibd
log scanned up to (1433402778)
[01] …done
[01] Copying ./wmaint/ORGTIER.ibd to /var/lib/mysql/backup/i1/./wmaint/ORGTIER.ibd
[01] …done
[01] Copying ./wmaint/PURCHASEORDERDETAIL.ibd to /var/lib/mysql/backup/i1/./wmaint/PURCHASEORDERDETAIL.ibd
[01] …done
[01] Copying ./wmaint/DEPARTMENT.ibd to /var/lib/mysql/backup/i1/./wmaint/DEPARTMENT.ibd
[01] …done
[01] Copying ./wmaint/PURCHASEORDERSUMMARY.ibd to /var/lib/mysql/backup/i1/./wmaint/PURCHASEORDERSUMMARY.ibd
[01] …done
[01] Copying ./wmaint/ORGNAICSCODE.ibd to /var/lib/mysql/backup/i1/./wmaint/ORGNAICSCODE.ibd
[01] …done
[01] Copying ./wmaint/REQWORKFLOWSTEPSSUMMARY.ibd to /var/lib/mysql/backup/i1/./wmaint/REQWORKFLOWSTEPSSUMMARY.ib d
[01] …done
[01] Copying ./wmaint/INVOICESUMMARY.ibd to /var/lib/mysql/backup/i1/./wmaint/INVOICESUMMARY.ibd
[01] …done
[01] Copying ./wmaint/ORGFINANCIALSYSTEM.ibd to /var/lib/mysql/backup/i1/./wmaint/ORGFINANCIALSYSTEM.ibd
[01] …done
[01] Copying ./wmaint/INVOICEDETAIL.ibd to /var/lib/mysql/backup/i1/./wmaint/INVOICEDETAIL.ibd
[01] …done
[01] Copying ./wmaint/BUSINESSUNIT.ibd to /var/lib/mysql/backup/i1/./wmaint/BUSINESSUNIT.ibd
[01] …done
[01] Copying ./wmaint/REQUISITIONDETAIL.ibd to /var/lib/mysql/backup/i1/./wmaint/REQUISITIONDETAIL.ibd
[01] …done
[01] Copying ./wmaint/BILL_INVOICEDETAIL.ibd to /var/lib/mysql/backup/i1/./wmaint/BILL_INVOICEDETAIL.ibd
[01] …done
log scanned up to (1433402778)
[01] Copying ./wmaint/DATEMASTER.ibd to /var/lib/mysql/backup/i1/./wmaint/DATEMASTER.ibd
[01] …done
[01] Copying ./wmaint/REQWORKFLOWFOLDERSSUMMARY.ibd to /var/lib/mysql/backup/i1/./wmaint/REQWORKFLOWFOLDERSSUMMARY. ibd
[01] …done
[01] Copying ./hobbitmonitor/variables.ibd to /var/lib/mysql/backup/i1/./hobbitmonitor/variables.ibd
[01] …done
[01] Copying ./hobbitmonitor/replicationmonitor.ibd to /var/lib/mysql/backup/i1/./hobbitmonitor/replicationmonitor. ibd
[01] …done
xtrabackup: The latest check point (for incremental): ‘1433402778’
xtrabackup: Stopping log copying thread.
.>> log scanned up to (1433402778)

xtrabackup: Transaction log of lsn (1433402778) to (1433402778) was copied.