Why can't you save in the FB Config area? Do you get a specific error message?
For the De-auth URL and general config, please make sure you hit the "Refresh" button in the top to update the latest settings. That may help you save as well.
As for 'will it cause issues', it depends. If authentication works on the front-end, then no, you should be good to go. There may just be some odd communication issue with Facebook. If auth doesn't work, there's an issue. If you still can't save your settings in Autotune, I'd recommend going to the Facebook Developer Area (where you created your API key) and edit your app directly. You can use all the recommended values that JFBConnect provides in the Autotune area and just plug them into the App configuration area.. that should definitely work.
I hope that helps,
Alex