Very spooky issue, but when I've been using Fileseek working on Magento which has a folder:
c:\approot\js\varien, all searches in varien fail.
When I rename the folder the searches work as normal, when I name back to varien, they fail..?

A reinstall fixed it...my laziness.

No, I was wrong. There really seems to be something spooking about having varien at the end of the folder path.
I tried a fresh install of Fileseek + a fresh source folder of magento (which contains path js/varien), searched for some known text with *.js, nothing. Changed the varien folder name to something else, and bingo, result comes back...??