Glad I could help! That is very odd.. I wonder why it’s using the one you made before then. Maybe by installing it, it made changes to your original setup? Another possibility, maybe it installed some sort of driver for the controller, I’m not to sure.
I didn’t have much time yesterday to mess with things (I just bought my Raspberry Pi). I remember watching on of Techtimpsta’s tutorial videos (he does tutorials for RetroPie setup), and I noticed something that may have to do with it?
In his PS1 emulator setup, he had to change some options in the emulator config to have his analog sticks work. Could there possibly be something similar for the SNES emulator and others?
Also, thinking about it, maybe its because these original game consoles didn’t have analog sticks obviously, so they are only looking for D-Pad input. Try mapping your analog stick inputs as D-Pad inputs and see if that works. I will be messing with my Pi later today and will report back if I find anything!!
EDIT: Literally as soon as I posted this, you changed your previous post to say the exact same thing ;D. Nice work!!!