Usually the server you are running metadata cleanup on is dead or can't replicate so that is normal.
Make sure you are at a good DC (not the one you are trying to delete)
Some other good links for the metadata cleanup are below:
http://www.petri.co.il/delete_failed_dcs_from_ad.htm
http://msmvps.com/blogs/ad/archive/2008/12/17/how-to-remove-a-failed-or-offline-dc.aspx
Thanks
Mike