Emulator Problem: Controller (Input)

I am using the final version of Jnes. My problem is that I run the setup for the controller (to set up the buttons) and after I close the program and then run it at a later time my configuration is gone (I have to run setup again). Is there a file that I can modify to make this be permanent (the default settings) ?

This sort of thing as been happening a lot on win 8.1 is that what you have? If not give us a few detail about your system.

My system is Win 7 Home Premium SP 1.