I had a strange problem the other day with search.  I was working with a SharePoint install after stsadm had been used to move the search index.  There were quite a few errors being thrown including errors about the index when we would go in and set up content sources.  We tried resetting everything in the Search settings, deleting and recreating SharedServices, all new databases and running the configuration wizard again and checked all permissions.  All of this was done to no avail.  It appeared that no matter what we did, the farm wasn’t moving over/recreating the index files in the new locations.

Finally, we removed the search server from the farm, ran a repair from the Windows Add/Remove Programs and re-ran the configuration wizard to re-join the server to the farm.  We made sure than the new file location for the index files was still set, and continued to re-setup everything to enable search.  Bingo!! That worked!!  So, if you are having problems with your search server no matter what you try, give this a shot.