Symptom: When you publish something to the topology in Lync 2010, you receive the following error:

The following machines from the topology you are publishing were not found in Active Directory and will result in errors during Enable-CsTopology as it tries to prepare Active Directory entries for the topology machines.  If you choose to publish this topology Enable-CsTopology will have to be re-run once the missing machines are domain-joined:

mymachine.mydomain

Solution: Exit out of the topology builder and relaunch it.  However, when you relaunch the topology builder, right click on it and Run as different user.  Type in your domain admin credentials.  You should now be able to successfully publish your topology.