dhg, Have you found a solution?
We are seeing this exact issue. It has been pretty widespread and random.
Windows 2008 R2 VMs behave exactly as you describe. Windows 2012 R2 VMs are more severely affected.
It has been impactful enough that we had to globally disable "Quiesce Guest File System and Applications". Absolutely 0 issues since that was disabled, but backups aren't as usable with that turned off.
We opened tickets with VMware, CommVault, and Microsoft and haven't made much progress. With Windows Server 2012 R2 VMs, they would actually hang in a state that was unresponsive to user requests, but may respond to a ping. We started monitoring for VMware Tools service state, and every morning some VMs would be reported as having VMware Tools as stopped (crashed). Since we disabled Quiesce this has not occurred once.
We've used multiple versions of VMware Tools (version 10246), ESXi (now on ESXi 6.0.0, 3620759), and Simpana 10 (now SP13+). I'm fairly certain most of the VMs affected are VM Version 8.
VMware seemed pretty confident that the issue affecting 2008 R2 is different than the issue affecting 2012 R2. They worked with us to try to highlight the 2012 R2 crash for Microsoft to try to debug / troubleshoot but we haven't found the magic combination yet. Any info you could add would be helpful.