Not sure what you mean by 'vanilla' file folders. Could you be more specific? A screenshot would be helpful also.
As for your Start menu search issues, have you checked to see if the index is running or complete, or is it paused or stopped? You can check via Control Panel/Indexing Options, as per the screenshot (note the red dots):
I would advise starting a new thread with the resulting info so that we can focus on the Explorer issue here.