Did you install the current bootloader, then "Upgrade and Erase"? If you did this and didn't skip steps, then the one thing I can suggest you try is to use a different SHORTER USB cable, then, right after plugging the USB in, plug 5V power (LIPO -> ESC -> servo connector) into an ESC connection. Then try saving some settings, reboot it and see if the settings stayed. The idea is that USB power may be weak and the battery would help that.