I just did this Windows 8 64 guest openSUSE 12.3 host. Upgrade (from WS 9.0.2 VMwre Tools} )nstalled without a hitch. just needed a reboot which it asked permission. In the VMwareTools on WS 9.0.2 I had enabled timesync (C:\"program files"\vmware\"Vmware Tools"\vmwaretoolboxcmd timesync enable. . Timesync remained enabled after the upgrade.
Did you perhaps try rebooting the guest from the VM power menu??