OK, so what is my problem? I don't know where else to look.

I tried again on my main backup drive. I launched the BiT GUI and clicked the snapshot icon to take a snapshot (Log-1). It seemed to work apart for a couple of warning with 5888 and 3072 errors. But BiT went through the complete process. Then when the next scheduled snapshot was due BIT got stuck again on compare with previous snapshot for an hour (Log-2). I then killed the python process and launched the BiT GUI and clicked the snapshot icon to take another snapshot and it worked again (Log-3). So it seems killing the python BiT process and taking another snapshot via the BiT GUi works but the scheduled snapshot doesn't. Also, I don't think the problem is that it's taking too long to compare snapshots because when I start a snapshot from the GUi it completes in about 30mins.

Log-1:

Jan 15 14:36:21 suntp001 backintime (Gxxxx): INFO: Lock
Jan 15 14:36:21 suntp001 backintime (Gxxxx): INFO: Include folders: ['/boot', '/srv', '/VAULT/Documents', '/home/Gxxxx', '/etc', '/usr/local', '/usr/lib', '/usr/share']
Jan 15 14:36:21 suntp001 backintime (Gxxxx): INFO: Ignore folders: []
Jan 15 14:36:21 suntp001 backintime (Gxxxx): INFO: Last snapshots: {}
Jan 15 14:36:21 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run]
Jan 15 14:36:21 suntp001 backintime (Gxxxx): INFO: Compare with old snapshot: 20100113-130225
Jan 15 14:36:22 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run] begin loop
Jan 15 14:37:08 suntp001 backintime (Gxxxx): WARNING: Command "rsync -aEAX  -i --dry-run  --chmod=Fa-w,D+w --whole-file --delete  --exclude="/media/Backup/TPX60s" --exclude="/home/Gxxxx/.local/share/backintime" --include="/boot/" --include="/srv/" --include="/VAULT/Documents/" --include="/VAULT/" --include="/home/Gxxxx/" --include="/home/" --include="/etc/" --include="/usr/local/" --include="/usr/" --include="/usr/lib/" --include="/usr/share/" --exclude="*.backup*" --exclude="*~" --exclude="/home/Gxxxx/.local/share/Trash/" --exclude="/home/Gxxxx/.gvfs" --exclude="/VAULT/Documents/WebSite" --exclude="/VAULT/Downloads" --include="/boot/**" --include="/srv/**" --include="/VAULT/Documents/**" --include="/home/Gxxxx/**" --include="/etc/**" --include="/usr/local/**" --include="/usr/lib/**" --include="/usr/share/**" --exclude="*" / "/media/Backup/TPX60s/backintime/20100113-130225/backup/"" returns 5888
Jan 15 14:37:08 suntp001 backintime (Gxxxx): INFO: Create hard-links
Jan 15 14:37:36 suntp001 backintime (Gxxxx): INFO: Command "cp -al "/media/Backup/TPX60s/backintime/20100113-130225/backup/"* "/media/Backup/TPX60s/backintime/new_snapshot/backup/"" returns 0
Jan 15 14:37:36 suntp001 backintime (Gxxxx): INFO: Call rsync to take the snapshot
Jan 15 14:50:45 suntp001 rsyslogd: -- MARK --
Jan 15 14:51:30 suntp001 smartd[4593]: Device: /dev/sda [SAT], SMART Usage Attribute: 194 Temperature_Celsius changed from 137 to 127
Jan 15 14:55:38 suntp001 backintime (Gxxxx): WARNING: Command "rsync -aEAX  -v --delete-excluded  --chmod=Fa-w,D+w --whole-file --delete  --exclude="/media/Backup/TPX60s" --exclude="/home/Gxxxx/.local/share/backintime" --include="/boot/" --include="/srv/" --include="/VAULT/Documents/" --include="/VAULT/" --include="/home/Gxxxx/" --include="/home/" --include="/etc/" --include="/usr/local/" --include="/usr/" --include="/usr/lib/" --include="/usr/share/" --exclude="*.backup*" --exclude="*~" --exclude="/home/Gxxxx/.local/share/Trash/" --exclude="/home/Gxxxx/.gvfs" --exclude="/VAULT/Documents/WebSite" --exclude="/VAULT/Downloads" --include="/boot/**" --include="/srv/**" --include="/VAULT/Documents/**" --include="/home/Gxxxx/**" --include="/etc/**" --include="/usr/local/**" --include="/usr/lib/**" --include="/usr/share/**" --exclude="*" / "/media/Backup/TPX60s/backintime/new_snapshot/backup/"" returns 3072
Jan 15 14:55:38 suntp001 backintime (Gxxxx): INFO: Save permissions
Jan 15 14:57:15 suntp001 backintime (Gxxxx): INFO: [smart remove] keep all >= 20100114-000000
Jan 15 14:57:15 suntp001 backintime (Gxxxx): INFO: [smart remove] keep first >= 20100104-000000 and < 20100111-000000
Jan 15 14:57:15 suntp001 backintime (Gxxxx): INFO: [smart remove] keep first >= 20091228-000000 and < 20100104-000000
Jan 15 14:57:15 suntp001 backintime (Gxxxx): INFO: [smart remove] keep snapshots: ['20100115-143621']
Jan 15 14:57:15 suntp001 backintime (Gxxxx): INFO: [smart remove] remove snapshot: 20100113-130225
Jan 15 14:57:34 suntp001 backintime (Gxxxx): INFO: Command "chmod -R a+rwx "/media/Backup/TPX60s/backintime/20100113-130225"" returns 0
Jan 15 14:57:46 suntp001 backintime (Gxxxx): INFO: Command "rm -rfv "/media/Backup/TPX60s/backintime/20100113-130225"" returns 0
Jan 15 14:57:46 suntp001 backintime (Gxxxx): INFO: [smart remove] remove snapshot: 20100112-142528
Jan 15 14:58:30 suntp001 backintime (Gxxxx): INFO: Command "chmod -R a+rwx "/media/Backup/TPX60s/backintime/20100112-142528"" returns 0
Jan 15 14:59:12 suntp001 backintime (Gxxxx): INFO: Command "rm -rfv "/media/Backup/TPX60s/backintime/20100112-142528"" returns 0
Jan 15 14:59:12 suntp001 backintime (Gxxxx): INFO: [smart remove] remove snapshot: 20100112-121613
Jan 15 14:59:45 suntp001 backintime (Gxxxx): INFO: Command "chmod -R a+rwx "/media/Backup/TPX60s/backintime/20100112-121613"" returns 0
Jan 15 15:00:01 suntp001 /usr/sbin/cron[23862]: (Gxxxx) CMD (nice -n 19 /usr/bin/backintime --backup-job >/dev/null 2>&1)
Jan 15 15:00:05 suntp001 backintime (Gxxxx): WARNING: A backup is already running
Jan 15 15:00:24 suntp001 backintime (Gxxxx): INFO: Command "rm -rfv "/media/Backup/TPX60s/backintime/20100112-121613"" returns 0
Jan 15 15:00:25 suntp001 backintime (Gxxxx): INFO: [smart remove] remove snapshot: 20100112-090001
Jan 15 15:00:57 suntp001 backintime (Gxxxx): INFO: Command "chmod -R a+rwx "/media/Backup/TPX60s/backintime/20100112-090001"" returns 0
Jan 15 15:01:31 suntp001 backintime (Gxxxx): INFO: Command "rm -rfv "/media/Backup/TPX60s/backintime/20100112-090001"" returns 0
Jan 15 15:01:31 suntp001 backintime (Gxxxx): INFO: Keep min free disk space: 200 Mb
Jan 15 15:01:33 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run] end loop
Jan 15 15:01:33 suntp001 backintime (Gxxxx): INFO: Unlock

Log-2:

Jan 15 16:00:03 suntp001 backintime (Gxxxx): INFO: Lock
Jan 15 16:00:03 suntp001 backintime (Gxxxx): INFO: Include folders: ['/boot', '/srv', '/VAULT/Documents', '/home/Gxxxx', '/etc', '/usr/local', '/usr/lib', '/usr/share']
Jan 15 16:00:03 suntp001 backintime (Gxxxx): INFO: Ignore folders: []
Jan 15 16:00:03 suntp001 backintime (Gxxxx): INFO: Last snapshots: {}
Jan 15 16:00:03 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run]
Jan 15 16:00:04 suntp001 backintime (Gxxxx): INFO: Compare with old snapshot: 20100115-143621
Jan 15 16:00:04 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run] begin loop

Log-3

Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: Lock
Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: Include folders: ['/boot', '/srv', '/VAULT/Documents', '/home/Gxxxx', '/etc', '/usr/local', '/usr/lib', '/usr/share']
Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: Ignore folders: []
Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: Last snapshots: {}
Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run]
Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: Compare with old snapshot: 20100115-143621
Jan 15 16:26:19 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run] begin loop
Jan 15 16:28:33 suntp001 backintime (Gxxxx): WARNING: Command "rsync -aEAX  -i --dry-run  --chmod=Fa-w,D+w --whole-file --delete  --exclude="/media/Backup/TPX60s" --exclude="/home/Gxxxx/.local/share/backintime" --include="/boot/" --include="/srv/" --include="/VAULT/Documents/" --include="/VAULT/" --include="/home/Gxxxx/" --include="/home/" --include="/etc/" --include="/usr/local/" --include="/usr/" --include="/usr/lib/" --include="/usr/share/" --exclude="*.backup*" --exclude="*~" --exclude="/home/Gxxxx/.local/share/Trash/" --exclude="/home/Gxxxx/.gvfs" --exclude="/VAULT/Documents/WebSite" --exclude="/VAULT/Downloads" --include="/boot/**" --include="/srv/**" --include="/VAULT/Documents/**" --include="/home/Gxxxx/**" --include="/etc/**" --include="/usr/local/**" --include="/usr/lib/**" --include="/usr/share/**" --exclude="*" / "/media/Backup/TPX60s/backintime/20100115-143621/backup/"" returns 5888
Jan 15 16:28:33 suntp001 backintime (Gxxxx): INFO: Create hard-links
Jan 15 16:28:55 suntp001 backintime (Gxxxx): INFO: Command "cp -al "/media/Backup/TPX60s/backintime/20100115-143621/backup/"* "/media/Backup/TPX60s/backintime/new_snapshot/backup/"" returns 0
Jan 15 16:28:55 suntp001 backintime (Gxxxx): INFO: Call rsync to take the snapshot
Jan 15 16:38:26 suntp001 backintime (Gxxxx): WARNING: Command "rsync -aEAX  -v --delete-excluded  --chmod=Fa-w,D+w --whole-file --delete  --exclude="/media/Backup/TPX60s" --exclude="/home/Gxxxx/.local/share/backintime" --include="/boot/" --include="/srv/" --include="/VAULT/Documents/" --include="/VAULT/" --include="/home/Gxxxx/" --include="/home/" --include="/etc/" --include="/usr/local/" --include="/usr/" --include="/usr/lib/" --include="/usr/share/" --exclude="*.backup*" --exclude="*~" --exclude="/home/Gxxxx/.local/share/Trash/" --exclude="/home/Gxxxx/.gvfs" --exclude="/VAULT/Documents/WebSite" --exclude="/VAULT/Downloads" --include="/boot/**" --include="/srv/**" --include="/VAULT/Documents/**" --include="/home/Gxxxx/**" --include="/etc/**" --include="/usr/local/**" --include="/usr/lib/**" --include="/usr/share/**" --exclude="*" / "/media/Backup/TPX60s/backintime/new_snapshot/backup/"" returns 5888
Jan 15 16:38:26 suntp001 backintime (Gxxxx): INFO: Save permissions
Jan 15 16:39:46 suntp001 backintime (Gxxxx): INFO: [smart remove] keep all >= 20100114-000000
Jan 15 16:39:46 suntp001 backintime (Gxxxx): INFO: [smart remove] keep first >= 20100104-000000 and < 20100111-000000
Jan 15 16:39:46 suntp001 backintime (Gxxxx): INFO: [smart remove] keep first >= 20091228-000000 and < 20100104-000000
Jan 15 16:39:46 suntp001 backintime (Gxxxx): INFO: [smart remove] keep snapshots: ['20100115-162619', '20100115-143621']
Jan 15 16:39:46 suntp001 backintime (Gxxxx): INFO: Keep min free disk space: 200 Mb
Jan 15 16:39:48 suntp001 backintime (Gxxxx): INFO: [KDE4Plugin.Systray.run] end loop
Jan 15 16:39:48 suntp001 backintime (Gxxxx): INFO: Unlock