Hi,
Did you upgrade VMware Tools or the virtual hardware on these VMs at any stage yet? Got any backups of the VMs to test with prior to the vSphere upgrade? The only bug I came across was reported in vSphere 5.0 update 2:
Remote Desktop IP virtualization might not work on a Windows Server 2008 R2 running on vSphere 4.0 Update 1
IP virtualization, which allows you to allocate unique IP addresses to RDP sessions, might not work on a Windows Server 2008 R2 64-bit vritual machine running on vSphere 4.0 Update 1. However, IP virtualization works when you configure Remote Desktop Services on a physical Windows Server 2008 R2 machine, or when you run a Windows Server 2008 R2 virtual machine on XenServer 5.5 Update 2 Dell OEM Edition.
This issue might occur if you install VMware Tools after installing Remote Desktop services.
Might be worth looking into VMware Tools on these VMs? Any AntiVirus changes? Sounds like Windows Explorer is caving on.....AV should scan on writes only if possible on RDS servers.
Regards,
Mike