@glook Thanks for the diagrams. Mine came with no papers at all and I followed the joystick orientation from the video (obviously wrong). My wiring was correct, but one joystick was mounted upside down. Knowing the joystick connector is "down" I could see which joystick was mounted wrong. It was strange it was always flipping the last configured joystick. All is working now 
Hi, I'm having some strange behavior after setting up Recalbox with Sanwa Joysticks and Dragonrise USB controllers and cannot figure it out. I'm following the instructions from ‪Arcade1UP Raspberry Pi Install Tutorial.
I'm 100% sure the USB controllers are wired the same. After configuring Joysitck+buttons for player 1 and 2 the up/down and left/right work correctly in the menus. The strange part is after I launch a game (fba_libretro or psx) the last controller I configured has left/right swapped and up/down swapped. They stay this way after exiting. Again, reconfigure and all works. Launch game and the last player configured has only the joystick swapped.
I have found two posts that kind of match my issue here and here. Changing recalbox.conf to "global.inputdriver=sdl2" did not help. I'm tech savvy and comfortable in linux. Here is recalbox-support output file. Many Thanks