This one comes up quite a bit, and causes one of those “wait, I know, I know, of course!” moments every time I’m about 85% through explaining the solution.
You want to index Adobe Acrobat files. You have installed the Adobe Acrobat iFilter on the index server, and you are able to successfully search for Acrobat files in the Portal. However, whenever you search for exactly the same Acrobat files from a team site, nothing comes back.
SharePoint Portal server is using a different search engine to the one used by WSS in team sites. SharePoint Portal Server uses SharePoint Search while WSS is using SQL Full-Text Search. Therefore to ensure Acrobat files are indexed and available in team sites you also have to install the Acrobat iFilter on the SQL Server. Of course! <grin>