Consider the following scenario:
You have a Microsoft SharePoint Server 2010 farm that has multi-crawl target Web Front Ends (WFEs).
You set up a search crawl for the farm by enabling the crawl target feature.
In this scenario, the search crawl does not use the crawl target WFEs to crawl the host header site collections. Instead, it uses Domain Name System (DNS) to resolve the host header site collections.
Note By default, the crawl target feature is not used for host header site collections. This feature is controlled by the AllowHostHeaderCrawlTarget search application setting.
To resolve this issue, apply this following hotfix package:
2459257 Description of the SharePoint Server 2010 Cumulative Update Server Hotfix Package (MOSS server-package): December 31, 2010
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.