Windows Server 2008 R2 and time sync issues seem to be more common than one would think. After poking around for a bit I was able to come up with a few steps to assist with that.

First we want to set the time server on the domain controllers, I like pool.ntp.org but the choice is up to you
w32tm /config /manualpeerlist:Pool.ntp.org /syncfromflags:manual /reliable:yes

We have no set it to use an external source and told it that we can use this server as a time server.

Lets restart the time services
net stop w32time
net start w32time

And finally synchronize the service
w32tm /resync

Well that part is completed, now lets move to the client servers.

This can be done manually by logging into each server if there is only a few, or creating a batch script to against them all.

We want to first stop the time service
net stop w32time

Now we want to remove all configurations from the registry
w32tm /unregister

And then reregister the new settings in the registry, this will pole the settings from the domain controller
w32tm /register

Now lets restart the service.
net start w32time

This should work for most of the domain member computers and it can be used to change that one server that keeps getting out of sync.