Safe Boot, (holding Shift key down at startup), does the problem occur in Safe Mode? Could take 10 minutes.
Safe mode attempts to repair Disks & clears lots of caches & loads safe Drivers, & prevents loading of 3rd party extensions, so if Safe Mode works try again in regular boot.
Manually Rebuilding Spotlight via Terminal
If the aforementioned Spotlight control panel approach doesn’t spur a reindexation of the drive, you may need to initiate it manually through the command line. Open Terminal and use the following command string to do so:
sudo mdutil -E /
This basically asks for temporary super user status, which is why Terminal may ask you for your password (it may not if you’ve used a sudo command recently or are already logged in as a super user or root. The command asks the unix tool mdutil to reindex the spotlight database for everything on the computer, including external drives, mounted disk images, etc. To re-index only for a specific drive, use the /Volumes path. For example, for an external drive named “MiniMe,” the command would look like this:
sudo mdutil -i on /
Rebuilding a drive index can take a long time, so be prepared to wait whether you do it through the System Preference panel or the command line.