(1) Are you using 'McAfee'? It has a known comptibility problem with Windows 7. If you are, try removing ~ not just disabling ~ it. Then rebuild the Index.
(2) Uncheck the attribute 'Folder is ready for archiving' in Advanced properties and attributes for files and folders (select from the right window of windows explorer NOT the folder tree). You must apply to all folders and subfolders. All files to be indexed again.
Click Here for location of above suggestions and maybe more possible solutions.