I noticed not only the up and down was different I also noticed when pressing left or right made the character jump up diagonally.
When installing my retroarch controller I had my d-pad, Analogstick and C-buttons overlap with eachother
If I remember correctly the c buttons on the N64 controller of the official game when pressed would give a diagonal jump in SSB. That could be a reason why the c buttons can’t overlap D-Pad and Analogstick directions.
I temporarily removed the following lines from my DragonRiseInc.GenericUSBJoystick.cfg