We had the exact issue as the OP with one of our 2012 R2 clusters, it will not get a list of VMs from the cluster, only the node you select in the VE backup job. I eventually had to create 2 separate MS VSS jobs to backup each node, so now when VMs change nodes I have to manually update my job.
Our 4 other Hyper-V clusters are still either 2008 R2 or 2012 but we use Veeam for them as DP was causing nothing but issues on the Cluster during backups so we had to find another solution that was stable. Granted this was 6.22/7.0 days but if you support something you should ensure it works before standing behind it.
I think DP should focus on fixing existing versions and adding support for existing Server OSs instead of moving all the way to DP 9 even though 8 is barely a year old.
Good luck.