I can confirm that the Issue is Windows Server 2016 related. We also have trouble with VM, which run with SQL Server Version 2014 to 2016. The problem is 100% not AD related, but it occurs when the checkpoint is merging. I was able to reproduce this issue with generating heavy IOs on a test VM and create / delete Checkpoints manuelly. Onward it dosen't matter on which Storage Subsystem the VM are located. We have this issue also with local SSD Storage.
I also think this is one more issue of Hyper-V 2016 and have opened a MS Support call, too
If I have any news, I let you know.