When you try to perform a crawl overlap in Microsoft SharePoint Server 2010 or in Microsoft SharePoint Foundation 2010, you notice that the start addresses of the content source cannot take ownership of the host header sites.
This issue occurs because the crawl overlap does not work correctly in the Host Header mode.
To resolve this issue, apply the following updates:
2276336 Description of the SharePoint Server 2010 hotfix package (osrchwfe-x-none.msp): August 31, 2010
2266423 Description of the SharePoint Foundation 2010 hotfix package (Sts-x-none.msp): August 31, 2010
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.