Hyper-V Core full server image with wbadmin

Firstly, there is a massive gotcha with Hyper-v and passthrough disks. You can not back them up normally through any kind of Hyper-V style back. The backup just ignores these disks and backs up the VHD.

For VHD backups, I'm currently trialling a method of taking VSS file system snapshots and then using these to pull consistent backups of the VHD files. Works pretty well for Windows machines due to the integration services. We do an export of the VM before it goes into the backup set so we can have a copy of the configs for importing. I'm also working on a way to only store VHD diffs to reduce backup storage requirements for 7 day rolling backups but it has yet to work properly.

With VSS, it will pause any machines that don't respond to the VSS aware query. Your ubuntu machine is one that'll be affected and probably have a few seconds of an outage during the backup while the snapshot happens.

It appears that a Windows Server 2008 R2 Hyper-V Host can back itself and all its Hyper-V machines up right out of the box. The shadow copy service appears capable without any additional help.