Okay, here's a snipplet from the ibbackup (via innobackup.pl) output. Note the file system errors about stat and directory. None of those files made it into the backup. Now that's an issue I've fixed. But what really was worrysome was that even with these errors, ibbackup and innobackup.pl told me the back was OK. See

090210  3:55:00  ibbackup: Full backup completed!
090210 03:55:04  innobackup: All tables unlocked
090210 03:55:04  innobackup: Connection to database server closed

innobackup: Backup created in directory '/backup/hot_backup/db2.actp/working/2009-02-09_22-01-38'
innobackup: MySQL binlog position: filename 'Warning', position (Code 1287): 'TYPE=storage_engine' is deprecated; use 'ENGINE=storage_engine' instead
090210 03:55:04  innobackup: innobackup completed OK!

090210  3:55:00  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/data/staging/DEBUG.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/EDGE_DAILY_SUMMARY.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/TOKEN.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/CAMPAIGN_IMAGE.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/CAMPAIGN_FIELD_MAPPING.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/CAMPAIGN_FIELD_VALUE_MAPPING.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/VOLUME_CAP_HISTORY.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/REIMPORT.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/MISSING_FIELD.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/ENTITY.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/EDGE.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/BAD_LEAD_SUMMARY_BACKUP.frm
InnoDB: File operation call: 'stat'.
090210  3:55:00  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/data/staging/EXTERNAL_VALIDATOR_CONFIG.frm
InnoDB: File operation call: 'stat'.

ibbackup: Compressed 283920 MB of data files to 67407 MB (compression 76%).

090210  3:55:00  ibbackup: Full backup completed!
090210 03:55:04  innobackup: All tables unlocked
090210 03:55:04  innobackup: Connection to database server closed

innobackup: Backup created in directory '/backup/hot_backup/db2.actp/working/2009-02-09_22-01-38'
innobackup: MySQL binlog position: filename 'Warning', position (Code 1287): 'TYPE=storage_engine' is deprecated; use 'ENGINE=storage_engine' instead
090210 03:55:04  innobackup: innobackup completed OK!