Hey buzz,
thanks for your reply. I have tested your suggestions:
* As I mentioned before, ES is not asking for controller reconfiguration after I press “Restart” inside of ES menu. But it does ask if I choose “Shutdown” and reboot by pulling out the plug and then back in.
* I also tried to press F4 (then a keyboard button to drop to terminal), then unplug and plug controller back in, wait some moments, and reload emulationstation. It still asks for reconfiguration of the “Logitech Cordless RumblePad 2″ 
* Then I tried to use a wired controller. With a wired controller everything works well. It only asks for configuration once and even after a power reset it keeps the configuration.
* I am not sure, but I seem to remember that had no such problems with the Beta 1.
Hopefully we will find a solution. It is really annoying and I am not the only one with this problem with F710,