I have just checked that atari800 uses (in a correct way) the SDL library to get joystick position.
I also assume that SDL has a correct implementation (proven in many project):
This means that your change was breaking compatibility not only with atari800 but with all games using the SDL library!
Sorry guys, but a proper place to fix your problem was your buggy Daphne emulator...
ControlBlock, PowerBlock & Co.