MacOS – Using FileVault 2 on non-boot disk with moved home directory

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.

The Recovery HD partition is not meant to be clone-able. They clearly failed and had no idea what they were doing when it came to that stage.

Running the Lion installer will install that Recovery HD partition properly. Please note that the Recovery HD partition is not required for Lion, but can be useful if you have any boot errors and need to reinstall Lion at a later date.

Re-installing Snow Leopard from a Lion install will not work, the user account details are slightly different between Snow Leopard and Lion (found that out the hard way), this would essentially render your user account useless.

Good Luck!

P.S. I'd advise you don't go back to that reseller, they have no clue what they're doing.

P.P.S. iampearce's comment about the drive being physically in the machine before installing Lion is irrelevant, and incorrect. The files that are used during the installer are loaded according to the machine hardware you boot from.