Are the values updating at all? Are the values on the right side of each field (our recommendations) showing in green or red? Is there any error message on the screen?
In general, usually there is an error message when values can't be saved. Facebook can dis-allow setting of values if all the steps in our configuration guide haven't been followed, especially setting the "Allow API Access to App Settings".
Beyond that, I don't have any immediate reasons as we haven't heard of this issue. If you're under time constraints, you can go to the Facebook Developer Area and copy the settings from Autotune into your application directly and save there. Not as easy, but you'll still be using the recommended settings from Autotune.
I hope that helps,
Alex