We have a custom STS implementation we are using in the company. SharePoint 2010 has a trust relation with this STS and all the websites (except central admin) is authenticated/authorized with this custom STS. All sites except central admin is claims based authentication sites.
The problem we are having is with the search crawl service account. In the central admin, when I try to change the service account, it only accepts windows AD accounts. We try extending the site and make the extended site windows authenticated site, however this time , crawler crawls the documents but does not differenciate the documents from different site collections within the site (for filtering). Anyone has any ideas?