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I faced this strange issue at one of my customers. They have medium size farm and have English and Arabic variations. Arabic variation is configured as source variation.
When we configure crawling content sources to site address as SharePoint Site, we noticed that SharePoint 2007 Indexer crawled only Arabic content of the site.
This can be caused by other things, but in our case, the problem was missing HTTP Response Header.
When a server joined to SharePoint Farm for Web Front End and Web Application is created, Internet Information Services is configured to have below HTTP Response Headers
MicrosoftSharePointTeamServices response header contains SharePoint version number.
If MicrosoftSharePointTeamServices is missing, SharePoint Indexer crawls only source variation site. Once it is added, Indexer crawled both variations properly.