@Toni
Preliminary test (besides the other GUI glitches I've reproduced...):
Use this remapped input devices config
https://gofile.io/d/bCffmy (some additional functions for the extra USB joystick buttons remapped to P, Space, Return, Ctrl...).
I use to start WinUAE with Hori Fighting Stick Mini plugged-in (Port2=Hori (Joystick mode))... play some WHDLoad game and then from Workbench I unplug the joystick and switch Game Port: Port2=Xbox controller (CD32 pad mode), play a game supporting CD32 pad like recent WHD installer for Barbarian II (Psygnosis).
Then I quit back to WB and switch again to joystick turning off XBox controller, and plugging in joystick before I switch to Port2=Hori (Joystick mode)...
Usually, at this point extra buttons assigns (P, Space, etc. mentioned at the beginning for the extra joystick buttons) are still listed from GUI but NOT WORKING.
To make them work again I have to RE-OPEN the GUI go to Input settings and just press OK to go back to emulation...
In brief strange things happens when I switch controller and settings from Game Ports. Sometimes WinUAE also totally resets my extra joystick button config after I switched back to it from XBox controller (CD32 mode).
Hope it's clear enough. If you can't reproduce it I'll try to do a repro-steps video.