...
At the time of writing, the default time server that is used by Windows 2008 R2 to sync its clock, time.windows.com, unfortunately is not (yet) reachable over IPv6.
But again , SURFnet comes to the rescue, because several of their NTP servers are IPv6-enabled. I picked chime3.surfnet.nl, which, according to the web interface, appears to be a Meinberg NTP server. Windows digs it all-right:
...
Unfortunately the Microsoft Update servers are also available only on IPv4 
.
I set-up a dual-stack limiting HTTP proxy server that listens on IPv6, and added a number of regular expressions to allow Windows updates to download updateshappen.
Details of the proxy and the Windows configuration process are described on a separate page.
...