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Sometimes index corruption or other problems with Windows Search cannot be fixed by the “Rebuild Index” option in the control panel.  One troubleshooting option you can try is to tell the indexer to reset the indexer to its out-of-the-box default setup.

For WDS 3.0 on Windows XP or Windows Vista:

1. Open Regedit.exe
2. Expand the HKEY_LOCAL_MACHINE node
3. Navigate to SOFTWARE \ MICROSOFT \ WINDOWS SEARCH
4. On the right-hand side of the screen, you should see a REG_SZ value named “SetupCompletedSuccessfully” which normally is set to a value of “1″.
5. Double-click on the value and change it to 0.
6. Restart the Windows Search service (either using the Services control panel, or the command line “net stop wsearch” followed by “net start wsearch”)

This will result in a rebuild of your index and will also reset your crawl scopes (folders to be indexed).  It may also reset certain Indexing-related settings.