When a VM host and guest OS both compete to control system time, anomolies can be introduced. In VM environments, this can either be done with the VM's daemon, or the client OS' daemon. Most virtualization experts agree the client OS should handle NTP. VMWare recommends that the guest OS time daemon controls the system clock.
VMWare ESXi 5.0+
For VMWare hosts, follow the steps in Timekeeping best practices for Windows, including NTP (1318) from VMWare. The section "VMware Tools Time Synchronization and Configuration" (section applies to any operating system) provides different ways to configure the VM host to disable time sync.