MacOS – How to encrypt the home folder

It's not an answer to your specific intermittent failure, but I do have a workaround that several clients have used.

I make them another account that isn't file vault protected and rather than logging out and leaving the mac at the welcome screen, enter the empty user and walk away. (or kick off a backup and then walk away)

In practice I get better backups when a user is logged in.

If this needs to work for you, do file a bug with apple since it should work each time and every time without a workaround. When it fails, there should be detailed enough logging to fix issues if they arise even if normal logs are suppressed as a compromise to added security with FileVault enabled.

Also BackupLoupe is great for poking at backups to see what is actually changing after the fact rather than guessing from logs and byte counts stored in logs.

I have had other people reconsider file vault and just use encrypted disk images for data that needs to be secured which minimizes many of the drawbacks of having the entire user folder inside file vault. I've done this myself since soon after file vault came out and I much prefer it compared to living with FileVault.

It's easier to just have each user store their private information in encrypted disk images since the old Filevault (1) method of encrypting the entire home folder isn't something you can set up on Lion with easy tools.

Lion does still support it, so you could migrate in a shell system that had the necessary accounts set up to use file vault, then encrypt the drive and finally move in the files from a backup external drive and presumably have both the legacy filevault storage scheme as well as the new scheme where the entire disk is unavailable until the drive password is entered.

Keep in mind - root (and any admin user that knows sudo) has total control of the system and can delete, remove any protection that was set by root. Using encryption with a distinct password is the only method to prevent root from actually making sense of the files it can easily access.