That's strange. Have you tried fixing permissions?
Although I doubt it'll fix your problem considering the latter issue, you could try going to the Menu Bar: Finder: Preferences: General tab, and selecting the box that says "Hard Disks". This will tell Finder to show hard disks.
If the two problems are just coincidental, the search fix may be achieved by going to System Preferences: Spotlight: Privacy and adding your HD to the list, logging out, logging in, and deselecting your HD from the list again. This would force Spotlight to update/create a new search base for itself.
Also, make sure that all your software is updated through Software Update to the latest versions.