Are you still looking for help with the in progress builds?
I’ve got an nv shield and it was doing similar goofy things. Gamepad wouldn’t be auto detected, wouldn’t save settings, and the history list wouldn’t work either.
For the history file, just create a file called “retroarch-content-history.txt” in the /data/data/com.retaroarch/ directory and make sure it’s read/write.
After that, the joysticks and gamepads aren’t working because a line in the retroarch.cfg file points to /autoconfig/android/… unfortunately, that directory is empty. I guess it’s a work in progress, but turns out that all of the regular gamepad configs are in the /autoconfig/ directory. I corrected the config but you might just as easily just copy all of the gamepad cfg files into the /autoconfig/android/ directory, and your gamepads will probably be auto detected and work again.
The last part is getting the config to not randomly change. I only half succeeded on that. I went line by line through the retroarch.cfg file fixing any problems I could find, and adjusting the settings by hand with a text editor. After that, using es (root) explorer, I took ownership of the config file and set it to read only and so far it hasn’t lost any settings.
One problem I still have, are the settings listed in /shared_prefs/com.retroarch_preferences.xml. That file seems to control the settings that are listed when you get into the preferences menu. It turns out that if you have a read only retroarch.cfg file, it will sorta override some of the incorrect settings, but I haven’t been able to get that preferences file to not get all goofy. So on mine, if you go into settings, it does randomly uncheck the custom save state and save games directories box, but it does actually still use them. Not great, but I like the additional options of the newer build.
If you decide to mess around with it again, hope this helps.