The point of FCP rescue is to quickly be able to restore your own preferences, like, how many auto saves, how many undos, where the windows appear and so on.
The first time you use it, press 'Trash Settings" and it takes your preferences back to factory settings. Easy, but all your little changes are now gone. So - then go through and set up FCP the way you like it. Then run FCP rescue again and choose 'Backup settings". This makes a copy of all your preferences for FCP - all the things you change in the settings from factory spec.
It should now say - settings in place - backup safe.
Next time you need to use it, choose trash settings and restore settings. This should replace the current (corrupt) settings with the clean backup set you made last time.