On our Intranet landing page search is configured and it is working, but under Site Collections that have their own content database, the search returns no results.
How can I configure search to work under those Site Collections.
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Check the Search Account used for content crawling. The account needs to have read access to the site collections and its databases. To do so open your Central Administration => Application Management => Manage Web Applications => Select Web Application of Site Collection which is not crawled correctly => User Policy => If Content Crawl Account is not listed here, add it.
If this does not solve your problem, check the Crawl Logs in Central Administration => Application Management => Manage Service Applications => Your Search Service Application => Crawl Log. Check the error messages.