During backup and you get an error saying Backing up Themes Failed the backup is timing out on your themes files.  This sometimes happens when customers have either a large number of files or extremely large files. This is very easy to do but might take a few attempts to find the correct number. Changing this setting impacts the  backup performance a bit so we want to try to find the highest number possible that will allow the backup to complete successfully.

 

In the settings section of WPBackItUp look for Batch Size then Themes Batch Size please adjust the value from 5000 to 4000 and run the backup again hopefully this will resolve the issue but if it doesn't  then try 3000, 2000 or 1000 until you find the correct number that will allow the backup to complete successfully. Click Save and run a backup.


http://support.wpbackitup.com/support/solutions/articles/5000675696-backing-up-themes-failed