Exported VM is missing primary disk and SATA Controller

[ghost]

This issue was originally opened by @jchodakowski as hashicorp/packer#4637. It was migrated here as a result of the Packer plugin split. The original body of the issue is below.

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Using virtualbox-iso builder, I am building a two disk VM with boot and main system on /dev/sda1 and /dev/sda2 and then /dev/sdb1 as a large LVM volume with various logical volumes mounted at various places on the file system. The disk is added using vboxmanage commands, and the build works as expected. In VirtualBox, you can inspect the VM and it has all the parts as described in the json template. Once the export happens however, the SATA controller is missing, as is the first of the two disks (sda). The second disk (sdb) is exported with the machine which, once re-imported has only an IDE disk controller, one disk, and won't boot (missing the system).

• Packer version: 0.12.3
• Host platform: Windows 10
• Guest platform: Ubuntu 14.04
• Debug log output: https://gist.github.com/jchodakowski/034b7961ab0b6162a1ff983a5f68e8fc
• Template: https://gist.github.com/jchodakowski/1b718595be804aa07ddadbfc220749d8
• Additional script 1 (ubuntu-14.04.cis.cfg [preseed]): https://gist.github.com/jchodakowski/bec5a86a8b6b1aedb72765ee9af2d328
• Additional script 2 (preseed_cfg): https://gist.github.com/jchodakowski/1f4ff13aa6a92926f6dbd5df2971b6a4
• Additional script 3 (lvm.sh): https://gist.github.com/jchodakowski/3ccf5fc96e6e78362ade56f7fe0dcf4b
• Additional script 4 (nessus.sh):
  Include these in your gist https://gist.github.com