I had the exact same issue and no idea what the cause was. After much messing around, several reinstalls and connecting to WiFi it worked. Even though I don't use the WiFi for some reason my PS3 pad wouldn't save until I connected to it. Not sure what the issue was but has worked perfectly since

Absolutely delighted with 4.0.0 beta and the only issue I have had so far is minor. I am using an original PS3 controller and have configured it by plugging it in via USB and then doing the controller configuration. When I select add a bluetooth controller in the menu it doesnt report any controllers found. However my pad works perfectly via bluetooth but  the red lights on the pad flash constantly instead of a single solid light. Is this correct?