Raspian Update causing ES mappings to reset constantly? - Pi3B Standard USB controllers

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Pi Model 3B
Power Supply used: adequate, 2.5Amps, 5.1V
RetroPie Version Used :4.2
Built From: retropie-4.2-rpi2_rpi3.img
USB Devices connected:standard USB gamepads + wireless keyboard

Ever since I ran the update scripts in RetroPie Setup, I noticed my controllers never remember their button mappings any more within Emulation Station. I ran through Configure Input and set up both Joypads again and again, but as soon as I launch any ROM, the joypad goes back to some unwanted mapping. Then I set it up again and the other Joypad loses it's settings. It's very frustrating.

Of course, I searched the forum and found a post on wiping the configuration files altogether to start again fresh. I did this. As promised, on rebooting the system brought up a fresh Configure Input wizard, which I dutifully went through for both joypads again ( and another two times on top of that) but the settings are never remembered.

I believe this has been triggered by the update process that updates Raspbian. I suspect this because I have two SD cards and this problem occurs on both.

Anyone else had this issue?

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I suspect this because I have two SD cards and this problem occurs on both.

Actually, that logic is flawed because different OS versions live on different cards... I am unsure of the cause.

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Problem Solved:
It turns out it was a wiring problem: the A and B Buttons were crossed on the 2nd controller. It seems the system has no way of differentiating between the two otherwise identical controllers. So the config for controller 2 probably overwrote the config for controller 1 and vice versa each time a new controller config was put in.