I have a 7 node 2012 R2 Hyper-V cluster (failover cluster) with SCVMM. The backend storage is a Netapp 2040-2, cluster-mode, and I'm using SMB 3.0 for my storage protocol. The hosts each have 4 1Gb bonded NICs using LACP and TransportPorts.
When I first setup the cluster, I did some testing from the guests and found that I could write to the storage at or near the speed of the network, 4Gb/s (512MB/s). This last week, applications started performing slowly and I found that I could now write to the storage at only about 30MB/s.
I checked the storage, network, found no problems or bottlenecks.
Finally, I created a VM directly on the hyper-v host which is has not been added as a resource to the failover cluster and was not created via SCVMM. This VM can write to the same storage (same volume, share, spindles, etc) at almost 4Gb/s. I can test simultaneously with any VM on any one of my 7 hyper-v hosts and it continues to have excellent IO performance and the VMs inside the cluster continue to have poor IO performance.
I have run packet traces to try to determine if anything could be wrong with the conversation between hyper-v and the storage, but found no issues.