this also happened to me in March/April of 2017 and I opened tickets with all vendors (Veeam, VMware, and Nimble). Eventually VMware said it was a bug and would be fixed in 6.0 P5. I converted the VM to VMFS and assumed it would be fixed.
Now, October 2017, I recently expanded a vVol VM from 6TB to 8TB and now I have the same problem snapshots timeout and have to be manually removed. Backups fail. and the VM goes offline for about 30 minutes every time a veeam backup job runs. I am already on ESXi 6.0 P5 so I think that the issue was not patched by VMware. I have opened a VMware ticket again.