Try logging in with another user account and see if you're having the same problem. If you don't have another user account, make one temporarily to test with.
I would try trashing the Finder's preferences file, "com.apple.finder.plist".
Your Spotlight may not have ever indexed this kind of system file, so you'll probably have to navigate to it manually. If you only have this problem with one user account, just trash that user's preference file, probably in the /Users/"YourName"/Library/Preferences folder, substituting "YourName" for your short user name.
While you're at it, trash your sidebar preferences file too, "com.apple.sidebarlists.plist"
It should be in the same folder.
If the problem appears to be system wide, try...