I use an Nvidia Shield controller mostly, but also a Dual Shock 3 and a Mad Catz generic Xbox 360 pad.
I’ve a USB n64 one and a mad catz xbox 360 and waiting get dual shock 3 when back in stock.
When I wanted to play N64 games in Retroarch (1.8.5) I noticed that in the game “Paper Mario” I could run only to down left, left and up left … I could only walk the other directions … This is also the case in other N64 games, with other consoles (NES, SNES, GB, GBC, GBA, GC, DS …) it was quite normal … I use the Switch Pro controller. I also made the sensitivity high in the quick menu and the dead line to 0. It would be nice if someone could help me and explain it easily.
Do you have ‘analog to digital type’ set to anything in settings > input? if so, it often interferes with movement in N64 games.
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My digital to analog type is “left analogstick”, is that worng?
here is a picture … It is now in German because I couldn’t change the language (hope that doesn’t bother). Do this pictures help or am I completely wrong because I am not so familiar with 
yeah, try setting that to ‘disabled’ or ‘none’ or whatever. What happens with N64 games is many of them accept input from both the dpad and the analog stick, but the analog stick actually gives directions that are opposite of what you’re pressing, so the dpad input cancels it out (mostly).
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Update: So … something strange has happened. I played a few Game Boy games and then I wanted to try the N64 games again. Now I can run in all directions again as if everything was normal. This is the case in all N64 games, except in Paper Mario … when I go down it goes down even though I don’t press anymore. Sometimes it is also that I push right or left and then it just runs down … I have not changed the settings :o
Thanks for helping 