I was messing around (through putty) in the options script and I selected the “Update input config…” item. Now my controller is unuseable. I tried recopying the dgenrc and retroarch.cfg in the all folder.
The Input Configuration Tool is developed by Aloshi, the developer of Emulation Station. You can find the Github site at https://github.com/Aloshi/ES-config and post possible bugs in the issue tracking category.