Symptom: When adding new field maps using TFS Bug Item Synchronzier admin and on the same time modifying TFS workitem template, this new modified template is not seen by the services, what's wrong?
TFS Explorer is using local cache in folder like this:
C:\Documents and Settings\%USERNAME%\Local Settings\Application Data\Microsoft\Team Foundation\2.0\Cache
This cache is refreshed when all connections are closed to server and new opened. So if you have some application (like sync admin) open, these new workitem template changes are not seen by the services.
So just close the admin and all other applications that connect to TFS server and this cache is refreshed during next connection. If you want to be sure that this cache is really refreshed, you can also manually delete this folder and all of its content.