Custom partition/disk configurations may conflict with Linode's managed backup service. I seem to remember that being mentioned but I could be wrong.
Edit:
viewtopic.php?p=28240#28240
Quote:
The backup system must be able to mount your disk images on the host. If you've used fdisk on your images to create partitions, or created encrypted volumes, or LVM, or done anything other than use our deployment or disk image creation tools, we won't be able to back up the data. The backup system operates on files, not at the block level.