This is a great utility, but unless I'm missing something, it appears not to be working as it did. The screen grab below shows the test I'm doing. Basically it finds nothing.
I re-installed an old version (1.9.1) to check, and with "Show folder name matches" ticked, it works as expected and finds the folder "beta". Unfortunately I don't have the previous version to compare with the current build. In case it is relevant this is running on Windows 7 x64.
I'm sorry for the introduction of this bug in the newer versions, I have just fixed it and released version 1.9.6. You can find the new version here: http://www.binaryfortress.com/fileseek/
Please let me know if you are still having any issues after installing 1.9.6. Thanks!