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 not possible (at least not that I know) to specify Filevault's target dir. It will work by automatically working with your home folder by creating (if you are in Leopard or above) a Sparse Bundle (or a Sparse Disk Image if you are in Tiger). The reason for the change has to do with Time Machine (and to allow -to a certain extent- to backup a FileVaulted home).
However, you can pretty much "replicate" the functionality of FileVault for a specific folder(s) by using Disk Utility to create an encrypted sparsebundle image of the Folder in question. You'd have to mount this image every time you want to use it but the "effect" is similar.
You can create symbolic links to the files and add the image to the login items if you have an application that needs the data in its original location (which is pretty common). You will possibly have to add the image password to the "Keychain" for it to be automatically expanded.
It would be important to read about Time Machine's limitations too, since a FileVault home directory can only occur when you're logging in (or out). In order to make Time Machine to act as a regular, you need OS X Server edition as a target.
According to the wikipedia entry (which I should have quoted at the beginning since it has all this information, better written and more complete):
FileVault is limited to encrypting home directories only in versions of Mac OS X prior to 10.7, and only those directories in their entirety. FileVault can encrypt entire disks starting with Mac OS X version 10.7
(emphasis added by me)
It remains to be seen whether this is true or not, since we don't speculate about future versions, but keep that in mind.
As an alternative, there are "multiple" programs that will also help you keep a secure "vault" of things. I'm mentioning Exces because I got it from a Bundle a couple of years ago. I used it three times and it works; there might be free alternatives (as well as using the plain "Disk Utility").
Update: Added the link provided by Kyle, because it explains how to do it, but kept my answer because it's "longer" :)
Best Answer
FileVault only encrypts one volume so hard links and firm links are encrypted (but firm links are portals to another volume which isn’t necessarily encrypted). Symbolic links exist on the volume and are encrypted, but their destination files are not encrypted - just the link to the other file is encrypted.
Your plan to move some folders off is just fine, solid technically and you can encrypt both volumes using FileVault and keep everything encrypted at rest - just that there are two different volumes with different keys and you choose if you use the same or different pass phrases for both.