I've found, while merging 3 accounts in to a fourth, the labels have a tendency to go bad when they're organized in levels.

eg:
Private
Private/mum
Private/Dad
Private/Dad/Holliday08
Private/Dad/Holliday09
Private/Dad/Holliday11

In this case, I found that mails stored in "Private" and "Private/Dad" would not get backed up.

I fixed this by running multiple backups and deleting folders (and consequently mails) in between.
Between 1st and 2nd run I would delete "Private/Dad/Holliday08", "Private/Dad/Holliday09", "Private/Dad/Holliday11" and "Private/mum". This allowed "Private/Dad" to get backed up.

I've reported this under "Bugs" not knowing if it's a feature ;)